U.S. patent application number 13/787450 was filed with the patent office on 2013-08-01 for system and method for identifying complex patterns of amino acids.
The applicant listed for this patent is Elenore S. Bogoch, Samuel Bogoch, Samuel Winston Bogoch, Anne-Elenore Bogoch Borsanyi. Invention is credited to Elenore S. Bogoch, Samuel Bogoch, Samuel Winston Bogoch, Anne-Elenore Bogoch Borsanyi.
Application Number | 20130195916 13/787450 |
Document ID | / |
Family ID | 46321948 |
Filed Date | 2013-08-01 |
United States Patent
Application |
20130195916 |
Kind Code |
A1 |
Bogoch; Samuel ; et
al. |
August 1, 2013 |
System and Method for Identifying Complex Patterns of Amino
Acids
Abstract
A method and system are disclosed for identifying and/or
locating complex patterns in an amino acid sequence stored in a
computer file or database. According to an aspect of the present
invention, techniques are provided to facilitate queries of protein
databases. For protein descriptions received in response to the
queries, embodiments of the present invention may scan the received
protein descriptions to identify and locate Replikin patterns. A
Replikin pattern is defined to be a sequence of 7 to about 50 amino
acids that include the following three (3) characteristics, each of
which may be recognized by an embodiment of the present invention:
(1) the sequence has at least one lysine residue located six to ten
amino acid residues from a second lysine residue; (2) the sequence
has at least one histidine residue; and (3) at least 6% of the
amino acids in the sequence are lysine residues.
Inventors: |
Bogoch; Samuel; (New York,
NY) ; Bogoch; Elenore S.; (New York, NY) ;
Borsanyi; Anne-Elenore Bogoch; (New York, NY) ;
Bogoch; Samuel Winston; (Oakland, CA) |
|
Applicant: |
Name |
City |
State |
Country |
Type |
Bogoch; Samuel
Bogoch; Elenore S.
Borsanyi; Anne-Elenore Bogoch
Bogoch; Samuel Winston |
New York
New York
New York
Oakland |
NY
NY
NY
CA |
US
US
US
US |
|
|
Family ID: |
46321948 |
Appl. No.: |
13/787450 |
Filed: |
March 6, 2013 |
Related U.S. Patent Documents
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12349955 |
Jan 7, 2009 |
8417462 |
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13787450 |
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11116203 |
Apr 28, 2005 |
7774144 |
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12349955 |
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10860050 |
Jun 4, 2004 |
7442761 |
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11116203 |
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10189437 |
Jul 8, 2002 |
7452963 |
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10860050 |
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10105232 |
Mar 26, 2002 |
7189800 |
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10189437 |
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Oct 26, 2001 |
7420028 |
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10105232 |
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Apr 28, 2004 |
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Feb 16, 2005 |
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Current U.S.
Class: |
424/209.1 ;
506/8 |
Current CPC
Class: |
C07K 14/27 20130101;
C07K 14/38 20130101; C07K 14/24 20130101; C07K 14/255 20130101;
C07K 14/31 20130101; C07K 14/37 20130101; C07K 14/36 20130101; C07K
14/21 20130101; C07K 14/285 20130101; G16B 15/00 20190201; C07K
14/195 20130101; C07K 14/28 20130101; C07K 14/33 20130101; C07K
14/405 20130101; C07K 14/34 20130101; C07K 14/22 20130101; C07K
14/205 20130101; C07K 14/39 20130101; C07K 14/005 20130101; C07K
14/26 20130101; C07K 14/355 20130101; C07K 14/40 20130101; C07K
14/305 20130101; C07K 14/44 20130101; C07K 14/245 20130101; G16B
35/00 20190201; A61K 2039/505 20130101; C07K 14/445 20130101; A61K
39/00 20130101; C12N 2760/16022 20130101; G16C 20/60 20190201; A61P
31/16 20180101; A61K 2039/53 20130101; G16B 30/00 20190201; A61K
38/00 20130101; C12N 2710/24122 20130101; C07K 14/30 20130101; C07K
14/35 20130101; C07K 14/335 20130101; C07K 14/415 20130101; C07K
14/345 20130101; C12N 2760/16122 20130101; C07K 14/315 20130101;
C07K 14/32 20130101; C07K 14/385 20130101; C07K 14/47 20130101 |
Class at
Publication: |
424/209.1 ;
506/8 |
International
Class: |
G06F 19/16 20060101
G06F019/16; C40B 30/02 20060101 C40B030/02 |
Claims
1-10. (canceled)
11. A method of recognizing a scaffolding structure of amino acids,
comprising: assembling a list of Replikin patterns occurring in a
plurality of proteins; and identifying the scaffolding structure as
a pattern of substantially fixed amino acid residues occurring in
each Replikin pattern in the list.
12. The method of claim 11, wherein the plurality of proteins
includes variants of the same protein.
13. The method of claim 11, wherein the plurality of proteins
includes different proteins.
14. A method of forecasting onset of disease, comprising:
determining a first count of Replikin patterns occurring in a
protein at a first time; determining a second count of Replikin
patterns occurring in the protein at a second time; and reporting
an increased probability of future disease caused by an organism
harboring the protein when the second count is greater than the
first count.
15. A method of synthesizing a vaccine, comprising: assembling a
list of Replikin patterns occurring in variants of a protein
associated with a disease-causing organism; identifying a
scaffolding structure of amino acids as a pattern of substantially
fixed amino acid residues occurring in each Replikin pattern in the
list; selecting elements of the scaffolding structure, wherein said
elements are conserved over time and wherein said elements are
represented in a current variant of the protein; and synthesizing a
vaccine based on the selected elements.
16. The method of claim 15, wherein the disease-causing organism is
influenza.
Description
RELATED APPLICATIONS
[0001] This application claims priority under 35 U.S.C.
.sctn.119(e) from U.S. Provisional Patent Application Ser. No.
60/565,847, filed Apr. 28, 2004 and entitled "SYSTEM AND METHOD FOR
IDENTIFYING COMPLEX PATTERNS OF AMINO ACIDS." This application also
claims priority under 35 U.S.C. .sctn.119(e) from U.S. Provisional
Patent Application Ser. No. 60/653,083, filed Feb. 16, 2005 and
entitled "SYSTEM AND METHOD FOR IDENTIFYING COMPLEX PATTERNS OF
AMINO ACIDS." Both of these provisional applications are
incorporated herein by reference in their entireties and for all
purposes.
[0002] Additionally, this application claims priority from and is a
Continuation In Part of U.S. Non-provisional patent application
Ser. No. 10/189,437, entitled "REPLIKIN PEPTIDES AND USES THEREOF,"
filed Jul. 8, 2002, which is a Continuation In Part of U.S.
Non-provisional patent application Ser. No. 10/105,232, entitled
"REPLIKIN PEPTIDES IN RAPID REPLICATION OF GLIOMA CELLS AND IN
INFLUENZA EPIDEMICS," filed Mar. 26, 2002, which is a Continuation
In Part of U.S. Non-provisional patent application Ser. No.
09/984,057, entitled "REPLIKINS AND METHODS OF IDENTIFYING
REPLIKIN-CONTAINING SEQUENCES," filed Oct. 26, 2001. Further, this
application claims priority from and is a Continuation In Part of
U.S. Non-provisional patent application Ser. No. 10/860,050,
entitled "REPLIKIN PEPTIDES AND USES THEREOF," filed Jun. 4, 2004.
All of these non-provisional applications are incorporated herein
by reference in their entireties and for all purposes.
TECHNICAL FIELD
[0003] This invention relates generally to the field of
bioinformatics. More particularly, the invention relates to
techniques for facilitating the identification of complex patterns
of nucleotide or amino acid sequences.
BACKGROUND OF THE INVENTION
[0004] As is well-known, amino acids are the building blocks of
proteins. Proteins make up the bulk of cellular structures, and
some proteins serve as enzymes for facilitating cellular reactions.
Twenty different amino acids are known to occur in proteins. The
properties of each protein are dictated in part by the precise
sequence of component amino acids.
[0005] Databases of amino acids and proteins are maintained by a
variety of research organizations, including, for example, the
National Center for Biotechnology Information (NCBI) at the U.S.
National Library of Medicine, and the Influenza Sequence Database
at the Los Alamos National Laboratory. These databases are
typically accessible via the Internet through web pages that
provide a researcher with capabilities to search for and retrieve
specific proteins. These databases may also be accessible to
researchers via local-area and wide-area networks. Additionally,
researchers may directly access amino acid and protein databases
stored on peripheral devices, such as magnetic disks, optical
disks, static memory devices, and a variety of other digital
storage media known in the art.
[0006] In amino acid and protein databases, amino acids are
typically encoded as alphabetic characters. FIG. 1 lists each amino
acid known to occur in proteins and provides a typical 3-letter
abbreviation and single-letter code by which the amino acids may be
represented in databases, according to a standard supplied by the
International Union of Pure and Applied Chemistry (IUPAC).
[0007] A given protein may be described by its sequence of amino
acids. For example, using the single-letter code given in FIG. 1,
the character string "crvpsgvdla" corresponds to the protein
defined by the following sequence of amino acids: cysteine,
arginine, valine, proline, serine, glycine, valine, aspartic acid,
leucine, and alanine.
[0008] When a protein database is searched for proteins that
satisfy certain criteria (for example, those proteins relating to
cancer in humans), the protein database search engine may respond
by identifying hundreds or thousands of matching proteins. This set
of matching proteins may be narrowed by supplying additional search
criteria. At any point during the search process, specific proteins
may be selected and reviewed. In FIG. 2, a printout describes a
specific protein identified from an NCBI search for proteins
relating to human cancer.
[0009] As can be seen in FIG. 2, a protein description may include
detailed information describing, among other identifying factors,
such information as the title of the protein ("Differential
expression of a novel serine protease homologue in squamous cell
carcinoma of the head and neck"), the authors of the protein
description ("Lang, J. C. and Schuller, D. E."), and the organism
from which the protein was isolated ("Homo sapiens").
[0010] Protein descriptions may include a specific sequence of
amino acids that define the protein. For example, in FIG. 2, amino
acid sequence data is found at the end of the description of the
protein, in a section of the printout prefaced by the word
"ORIGIN." In this example, the first few amino acids are
"myrpdvvrar," which correspond to methionine, tyrosine, arginine,
proline, aspartic acid, valine, valine, arginine, alanine, and
arginine.
[0011] Some protein descriptions may include a sequence of nucleic
acid bases, rather than amino acid sequences, that define the
protein. As is known, a sequence of three nucleic acid bases (i.e.,
a nucleic acid base triplet) may correspond to an amino acid
according to a mapping provided by the table found in FIG. 3. Each
nucleic acid base triplet identified in the table represents or
corresponds to a specific amino acid. For example, the nucleic acid
triplet GCT (guanine-cytosine-thymine) corresponds to the amino
acid Alanine. Similarly, the nucleic acid triplet GCA
(guanine-cytosine-adenine) also corresponds to the amino acid
Alanine. As another example, the nucleic acid triplets AAA and AAG
(adenine-adenine-adenine and adenine-adenine-guanine, respectively)
each corresponds to the amino acid Lysine.
The Replikin Pattern
[0012] In previous patent applications, the inventors have
identified and described a pattern of amino acids that has been
designated a "Replikin pattern" or simply a "Replikin." A Replikin
pattern comprises a sequence of about 7 to about 50 contiguous
amino acids that includes the following three (3)
characteristics:
[0013] (1) the sequence has at least one lysine residue located six
to ten amino acid residues from a second lysine residue;
[0014] (2) the sequence has at least one histidine residue; and
[0015] (3) the sequence has at least 6% lysine residues.
[0016] Replikins have been shown to be associated with rapid
replication in fungi, yeast, viruses, bacteria, algae, and cancer
cells. Based on this association, it is believed that Replikins may
be an indicator of disease. Additionally, an increase in
concentration of Replikins over time may be an indicator of the
imminent onset of disease. For example, before each of the three
influenza pandemics of the last century (identified as H1N1, H2N2
and H3N2), there was a significant increase in the concentration of
Replikins in the corresponding influenza virus. With respect to the
H5N1 influenza, FIG. 4 illustrates a rapid increase in the
concentration of Replikins per 100 amino acids just prior to
epidemics in 1997 (indicated as E1), 2001 (indicated as E2) and
2004 (indicated as E3). Replikin patterns have been found in a
variety of disease-related proteins, including cancers of the lung,
brain, liver, soft-tissue, salivary gland, nasopharynx, esophagus,
stomach, colon, rectum, gallbladder, breast, prostate, uterus,
cervix, bladder, eye, forms of melanoma, lymphoma, leukemia, and
kidney. Importantly, Replikin patterns appear to be absent from the
normal healthy human genome. FIG. 5 lists selected examples of
Replikin patterns that have been found in various organisms.
[0017] For example, the 13-residue pattern "hyppkpgcivpak,"
occurring in Hepatitis C (which is the last entry in the Tumor
Virus Category of FIG. 5) is a Replikin pattern because: (1) it
contains two lysine residues that are 8 positions apart; (2) it
contains a histidine residue; and (3) the percentage of lysine
residues is 2/13, which is 15.4%.
Amino Acid Search Tools
[0018] As is known in the art, databases of proteins and amino
acids may be searched using a variety of database tools and search
engines. Using these publicly available tools, patterns of amino
acids may be described and located in many different proteins
corresponding to many different organisms. Several methods and
techniques are available by which patterns of amino acids may be
described. One popular format is the PROSITE pattern. A PROSITE
pattern description may be assembled according to the following
rules:
[0019] (1) The standard International Union of Pure and Applied
Chemistry (IUPAC) one-letter codes for the amino acids are used
(see FIG. 1).
[0020] (2) The symbol `x` is used for a position where any amino
acid is accepted.
[0021] (3) Ambiguities are indicated by listing the acceptable
amino acids for a given position, between square parentheses if.
For example: [ALT] would stand for Alanine or Leucine or
Threonine.
[0022] (4) Ambiguities are also indicated by listing between a pair
of curly brackets `{ }` the amino acids that are not accepted at a
given position. For example: {AM} stands for any amino acid except
Alanine and Methionine.
[0023] (5) Each element in a pattern is separated from its neighbor
by a `-`.
[0024] (6) Repetition of an element of the pattern can be indicated
by following that element with a numerical value or a numerical
range between parenthesis. Examples: x(3) corresponds to x-x-x,
x(2,4) corresponds to x-x or x-x-x or x-x-x-x.
[0025] (7) When a pattern is restricted to either the N- or
C-terminal of a sequence, that pattern either starts with a `<`
symbol or respectively ends with a `>` symbol.
[0026] (8) A period ends the pattern.
[0027] Examples of PROSITE patterns include:
[0028] PA [AC]-x-V-x(4)-{ED}. This pattern is translated as:
[Alanine or Cysteine]-any- Valine -any-any-any-any-{any but
Glutamic Acid or Aspartic Acid}
[0029] PA<A-x-[ST](2)-x(0,1)-V. This pattern, which must be in
the N-terminal of the sequence (`<`), is translated as: Alanine
-any-[Serine or Threonine]-[Serine or Threonine]-(any or
none)-Valine.
[0030] Another popular format for describing amino acid sequence
patterns is the regular expression format that is familiar to
computer scientists. In computer science, regular expressions are
typically used to describe patterns of characters for which finite
automata can be automatically constructed to recognize tokens in a
language. Possibly the most notable regular expression search tool
is the Unix utility grep.
[0031] In the context of describing amino acid sequence patterns, a
simplified set of regular expression capabilities is typically
employed. Amino acid sequence patterns defined by these simple
regular expression rules end up looking quite similar to PROSITE
patterns, both in appearance and in result. A regular expression
description for an amino acid sequence may be created according to
the following rules:
[0032] (1) Use capital letters for amino acid residues and put a
"-" between two amino acids (not required).
[0033] (2) Use "[ . . . ]" for a choice of multiple amino acids in
a particular position. [LIVM] means that any one of the amino acids
L, I, V, or M can be in that position.
[0034] (3) Use "{ . . . }" to exclude amino acids. Thus, {CF} means
C and F should not be in that particular position. In some systems,
the exclusion capability can be specified with a " " character. For
example, G would represent all amino acids except Glycine, and [
ILMV] would represents all amino acids except I, L, M, and V.
[0035] (4) Use "x" or "X" for a position that can be any amino
acid.
[0036] (5) Use "(n)", where n is a number, for multiple positions.
For example, x(3) is the same as "xxx".
[0037] (6) Use "(n1,n2)" for multiple or variable positions. Thus,
x(1,4) represents "x" or "xx" or "xxx" or "xxxx".
[0038] (7) Use the symbol ">" at the beginning or end of the
pattern to require the pattern to match the N or C terminus. For
example, ">MDEL" finds only sequences that start with MDEL.
"DEL>" finds only sequences that end with DEL.
[0039] The regular expression, "[LIVM]-[VIC]-x
(2)-G-[DENQTA]-x-[GAC]-x (2)-[LIVMFY](4)-x (2)-G" illustrates a 17
amino acid peptide that has: an L, I, V, or M at position 1; a V,
I, or C at position 2; any residue at positions 3 and 4; a G at
position 5 and so on . . . .
[0040] Other similar formats are in use as well. For example, the
Basic Local Alignment Search Tool (BLAST) is a well-known system
available on the Internet, which provides tools for rapid searching
of nucleotide and protein databases. BLAST accepts input sequences
in three formats: FASTA sequence format, NCBI Accession numbers, or
GenBank sequence numbers. However, these formats are even more
simple in structure than regular expressions or PROSITE patterns.
An example sequence in FASTA format is:
TABLE-US-00001 >gi|532319|pir|TVFV2E|TVFV2E envelope protein
ELRLRYCAPAGFALLKCNDADYDGFKTNCSNVSVVHCTNLMNTTVTTGLLLNGSYSENRT
QIWQKHRTSNDSALILLNKHYNLTVTCKRPGNKTVLPVTIMAGLVFHSQKYNLRLRQAWC
HFPSNWKGAWKEVKEEIVNLPKERYRGTNDPKRIFFQRQWGDPETANLWFNCHGEFFYCK
MDWFLNYLNNLTVDADHNECKNTSGTKSGNKRAPGPCVQRTYVACHIRSVIIWLETISKK
TYAPPREGHLECTSTVTGMTVELNYIPKNRTNVTLSPQIESIWAAELDRYKLVEITPIGF
APTEVRRYTGGHERQKRVPFVXXXXXXXXXXXXXXXXXXXXXXVQSQHLLAGILQQQKNL
LAAVEAQQQMLKLTIWGVK
[0041] Features of the BLAST system include sequence comparison
algorithms that are used to search sequence databases for regions
of local alignments in order to detect relationships among
sequences which share regions of similarity. However, the BLAST
tools are limited in terms of the structure of amino acid sequences
that can be discovered and located. For example, BLAST is not
capable of searching for a sequence that has "at least one lysine
residue located six to ten amino acid residues from a second lysine
residue," as required by a Replikin pattern, for example. Nor is
BLAST capable of searching for amino acid sequences that contain a
specified percentage or concentration of a particular amino acid,
such as a sequence that has "at least 6% lysine residues."
Need for Replikin Search Tools
[0042] As can be seen from its definition, a Replikin pattern
description cannot be represented as a single linear sequence of
amino acids. Thus, PROSITE patterns and regular expressions, both
of which are well suited to describing ordered strings obtained by
following logical set-constructive operations such as negation,
union and concatenation, are inadequate for describing Replikin
patterns.
[0043] In contrast to linear sequences of amino acids, a Replikin
pattern is characterized by attributes of amino acids that
transcend simple contiguous ordering. In particular, the
requirement that a Replikin pattern contain at least 6% lysine
residues, without more, means that the actual placement of lysine
residues in a Replikin pattern is relatively unrestricted. Thus, in
general, it is not possible to represent a Replikin pattern
description using a single PROSITE pattern or a single regular
expression.
[0044] Accordingly, there is a need in the art for a system and
method to scan a given amino acid sequence and identify all
instances of a Replikin pattern. Similarly, there is a need in the
art for a system and method to search protein databases and amino
acid databases for amino acid sequences that match a Replikin
pattern. Additionally, there is a need in the art for a generalized
search tool that permits researchers to locate amino acid sequences
of arbitrary specified length that includes any desired combination
of the following characteristics: (1) a first amino acid residue
located more than N positions and less than M positions away from a
second amino acid residue; (2) a third amino acid residue located
anywhere in the sequence; and (3) the sequence contains at least R
percent of a fourth amino acid residue. Finally, the shortcomings
of the prior art are even more evident in research areas relating
to disease prediction and treatment. There is a significant need in
the art for a system to predict in advance the occurrence of
disease (for example, to predict strain-specific influenza
epidemics) and similarly to enable synthetic vaccines to be
designed based on amino acid sequences or amino acid motifs that
are discovered to be conserved over time and which have not been
previously detectable by prior art methods of searching proteins
and amino acid sequences.
BRIEF DESCRIPTION OF THE DRAWINGS
[0045] FIG. 1 is a conversion table that enables amino acids to be
encoded as single alphabetic characters according to a standard
supplied by the International Union of Pure and Applied Chemistry
(IUPAC).
[0046] FIG. 2 is a printout of a human cancer protein obtained by
searching a protein database maintained by the National Center for
Biotechnology Information (NCBI).
[0047] FIG. 3 is a conversion table illustrating a correspondence
between nucleic acid base triplets and amino acids.
[0048] FIG. 4 is a graph illustrating a rapid increase in the
concentration of Replikin patterns in a selected strain of
Hemagglutinin prior to the outbreak of three "Bird Flu"
epidemics.
[0049] FIG. 5 is a table illustrating selected examples of Replikin
patterns that have been found in various organisms.
[0050] FIG. 6 is a high-level block diagram of a computer system
incorporating a system and method for identifying Replikin patterns
in amino acid sequences, in accordance with an embodiment of the
present invention.
[0051] FIG. 7 is a simple flow chart illustrating a general method
for locating a Replikin pattern in a sequence of amino acids,
according to an embodiment of the present invention.
[0052] FIG. 8 is a flow chart illustrating a generalized method for
locating a plurality of Replikin-like patterns in a sequence of
amino acids, according to an embodiment of the present
invention.
[0053] FIG. 9 is a source code listing containing a procedure for
discovering Replikin patterns in a sequence of amino acids, in
accordance with an embodiment of the present invention.
[0054] FIG. 10. is a table illustrating Replikin scaffolds
occurring in substantially fixed amino acid positions in different
proteins.
[0055] FIG. 11 is a simplified block diagram of a computer system
platform useful with the present invention.
DETAILED DESCRIPTION
[0056] Embodiments of the present invention are directed to a
system and method for identifying and/or locating complex patterns
in an amino acid sequence. According to an aspect of the present
invention, techniques are provided to facilitate queries of protein
databases. For protein descriptions received in response to the
queries, embodiments of the present invention may scan the received
protein descriptions to identify and locate Replikin patterns.
According to an embodiment, a Replikin pattern is a sequence of
from 7 to about 50 amino acids that include the following three (3)
characteristics, each of which may be recognized by an embodiment
of the present invention: (1) the sequence has at least one lysine
residue located six to ten amino acid residues from a second lysine
residue; (2) the sequence has at least one histidine residue; and
(3) at least 6% of the amino acids in the sequence are lysine
residues. Another embodiment of the present invention may identify
and/or locate a complex amino acid sequence having specified length
constraints, which further includes any combination of the
following characteristics: (1) a first amino acid residue located
more than N positions and less than M positions away from a second
amino acid residue; (2) a third amino acid residue located anywhere
in the sequence; and (3) at least R percent of a fourth amino acid
residue. According to yet another embodiment, the present invention
may count occurrences of the identified amino acid sequences and
may report the counted occurrences, either as raw absolute values
or as ratios of the number of identified amino acid sequences per N
amino acids in the protein. Still another embodiment of the present
invention may analyze the evolution of identified amino acid
sequence patterns in variants of a given protein over time, and may
also analyze the similarities and differences between instances of
identified amino acid sequence patterns across a plurality of
different proteins over time. As a result of the analysis, yet
another embodiment of the present invention may identify potential
amino acid scaffolding structures that appear to be preserved over
time and across different proteins, as component elements of the
identified amino acid sequence patterns mutate and/or evolve.
[0057] Embodiments of the present invention will be described with
reference to the accompanying drawings, wherein like parts are
designated by like reference numerals throughout, and wherein the
leftmost digit of each reference number refers to the drawing
number of the figure in which the referenced part first
appears.
[0058] FIG. 6 is a high-level block diagram of a computer system
incorporating a system and method for identifying Replikin patterns
in amino acid sequences, in accordance with an embodiment of the
present invention. As shown in FIG. 6, computer workstation 610 may
be a computer having a processor and a memory configured to permit
a researcher to search protein databases and to scan protein
descriptions for selected amino acid patterns. To accomplish these
functions, computer workstation 610 may include protein and amino
acid research system 630, which may receive instructions from a
user/researcher to conduct protein searching and amino acid
scanning operations. According to an embodiment, protein and amino
acid research system 630 may further include amino acid sequence
scanner 640 that scans and searches retrieved protein and amino
acid sequences for specific patterns of amino acids, including
Replikin patterns. Protein and amino acid research system 630 may
communicate with network interface 620 to obtain protein sequences
and amino acid sequences from resources on network 660, which may
include the Internet. Alternatively, protein and amino acid
research system 630 may obtain protein sequences and amino acid
sequences from a local protein database 650. In addition, protein
and amino acid research system 630 may obtain protein sequences and
amino acid sequences directly from other input means, such as
keyboard input. Protein and amino acid research system 630 may also
communicate with network interface 620 to transmit results to other
computers on network 660.
Scanning for Replikin Patterns
[0059] Embodiments of the present invention may include a
generalized method and system for identifying complex patterns of
amino acids within proteins. For any protein definition identified
or selected by protein and amino acid research system 630, the user
may direct embodiments of the invention to search for a variety of
complex patterns of amino acids. As an example of one pattern of
amino acids, the present invention provides a method for
identifying nucleotide or amino acid sequences that include a
Replikin pattern. FIG. 7 is a simple flow chart illustrating a
general method for locating a Replikin pattern in a sequence of
amino acids, according to an embodiment of the present invention.
The method 700 may begin after a sequence of amino acids has been
obtained. Typically, the sequence of amino acids may be represented
by alphabetic characters according to the code supplied in FIG. 1.
However, other encodings are envisioned by the present invention as
well.
[0060] Referring to FIG. 7, once a sequence of amino acids has been
obtained, the sequence is searched for a Replikin pattern (710),
which comprises a subsequence (or string) of amino acids that
includes the following characteristics:
[0061] (1) the string contains from 7 to about 50 amino acids;
[0062] (2) the string contains at least one lysine residue located
6 to 10 positions from a second lysine residue;
[0063] (3) the string contains at least one histidine residue;
and
[0064] (4) the string contains at least 6% lysine residues.
[0065] Once a string of amino acids is found to match the Replikin
pattern, the string may be identified or marked (720)
accordingly.
[0066] A given sequence of amino acids may contain many
subsequences or strings that match the Replikin pattern.
Additionally, Replikin patterns may overlap each other. Thus, to
locate and identify all possible Replikin patterns in a sequence of
amino acids, method 700 may be invoked iteratively for each
subsequence of amino acids contained within the original sequence
of amino acids.
[0067] When method 700 is invoked iteratively to identify and
locate all possible Replikin patterns in an amino acid sequence, an
embodiment of the present invention may count the number of
resulting Replikin patterns. A Replikin count may be reported as an
absolute number. Additionally, embodiments of the invention may
also determine a ratio of the number of Replikins per N amino acids
in the sequence. For example, an embodiment may determine that a
given protein contains a ratio of 6 Replikins for every 100 amino
acids. Replikin ratios have been shown by laboratory experiment and
by epidemiological evidence to correlate directly to the rate that
a given protein replicates. Rapid replication of proteins may be an
indication of disease. For example, the presence of relatively high
ratios of Replikin patterns has been correlated to epidemics of
influenza. Similarly, an increase in the count of Replikin patterns
observed in a protein over time may also be an indication of future
disease caused by the organism from which the protein was obtained
(see, e.g., FIG. 4). Thus, the ability to detect and count Replikin
patterns within sequences of amino acids is a significant advantage
of the present invention.
[0068] Still referring to FIG. 7, embodiments of the present
invention may utilize method 700 to identify and locate other
complex patterns of amino acids, which exhibit characteristics
similar to Replikin patterns. That is, although some embodiments of
the present invention may specify exact values for: (1) distances
between amino acids, (2) acceptable lengths of recognized amino
acid sequences, and (3) the percentage or concentration of specific
amino acids, these exact values may also be expressed as variables.
Thus a researcher may employ an embodiment of the present invention
to identify sequences of amino acids in a protein that have the
following characteristics:
[0069] (1) the sequence contains from rmin to rmax amino acids;
[0070] (2) the sequence contains at least one lysine residue
located kmin to kmax amino acid residues from a second lysine
residue;
[0071] (3) the sequence contains at least one histidine residue;
and
[0072] (4) the sequence contains at least kpercent lysine
residues.
[0073] FIG. 8 is a flow chart illustrating a generalized method 800
for locating a plurality of Replikin-like patterns in a given
sequence of amino acids, according to an embodiment of the present
invention. The method 800 begins by locating a first lysine residue
in the given sequence (810). Then, the method 800 may determine
whether a second lysine residue resides within kmin to kmax
positions of the first lysine residue (820). As indicated in FIG.
8, kmin and kmax define the limits on the distance between the
first and second lysine residues. For a typical Replikin pattern,
kmin will equal 6 and kmax will equal 10. However, these values may
be varied by a researcher interested in discovering other similar
patterns.
[0074] Once method 800 has identified two lysine residues that are
close enough to each other (820), the method 800 may examine every
histidine residue that resides within rmax positions of both the
first and second lysine residues (830). When method 800 is employed
to identify and locate typical Replikin patterns, rmax will usually
be set to equal 50. For every histidine residue that resides within
rmax positions of the two lysine residues identified in steps (810)
and (820), method 800 will construct the shortest string of amino
acid residues that includes the first lysine residue, the second
lysine residue, and the identified histidine residue (840). Then,
method 800 will determine whether the length of that shortest
string is within the desired range--that is, whether it contains at
least rmin amino acid residues and no more than rmax amino acid
residues (850). Finally, if the identified string of amino acids
also contains at least kpercent of lysine residues (860), the
string will be identified as matching the desired Replikin-like
pattern (870).
[0075] Still referring to FIG. 8, it is apparent that method 800
may identify several Replikin-like patterns from a single given
amino acid sequence. This may happen because method 800 may examine
more than one histidine residue that resides within rmax positions
of the two identified lysine residues. Each identified histidine
residue may, in combination with the two lysine residues, match the
desired Replikin-like pattern.
[0076] One embodiment of the method illustrated by FIG. 8 is shown
in FIG. 9, which is a source code listing containing a procedure
for discovering all Replikin patterns present in a given sequence
of amino acids, in accordance with an embodiment of the present
invention. The "match" procedure shown in FIG. 9 is programmed in
an interpreted shell language called "Tcl" and recognizes Replikins
in a straightforward fashion. As known in the art, the "Tool
Command Language" or Tcl (pronounced "tickle") is a simple
interpreted scripting language that has its roots in the Unix
command shells, but which has additional capabilities that are
well-suited to network communication, Internet functionality and
the rapid development of graphical user interfaces.
[0077] Alternative methods of recognizing Replikin patterns are
also covered by the teachings of the present invention. For
example, the match procedure shown in FIG. 9 could be implemented
in other programming languages such as Java or C or C++.
Additionally, alternative embodiments of the Replikin recognizing
algorithm may identify the characteristics of a Replikin pattern in
any order, and may also traverse component amino acid sequences and
subsequences using recursive techniques, iterative techniques,
parallel processing techniques, divide-and-conquer techniques or
any combination thereof.
Protein Search Engine
[0078] Returning to FIG. 6, the present invention may include a
search engine to access and interact with amino acid and protein
databases, either locally or over a network such as the Internet,
to retrieve protein definitions. For example, protein and amino
acid research system 630 may accept protein search criteria from a
user, and may then access a plurality of on-line amino acid and
protein database search engines to retrieve protein definitions
that match the supplied search criteria. Protein database search
criteria may comprise any text string that may form a valid search
term in any of the on-line protein or amino acid search engines.
Typically, these search criteria relate to text that may be found
in the printout that describes each specific protein. For example,
if the user supplied the search criteria "influenza type A,"
embodiments of the present invention may forward this text string
to a plurality of Internet protein and amino acid search engines,
each of which may then return any protein descriptions found in
their databases that contained the terms "influenza type A."
Employing amino acid sequence scanner 640, each of the returned
protein descriptions may be scanned for the presence of Replikin
patterns.
[0079] Additional embodiments of the present invention may permit a
user to select or de-select a plurality of Internet protein search
engines and to customize the search criteria and protein retrieval
capabilities of the present invention for each of the selected
on-line protein search engines. Moreover, embodiments of the
invention may also permit a user to access a local protein database
650 or to supply a specific protein definition directly, for
example, by supplying a local file name containing the protein
definition, or by other methods known in the art for supplying
parameters to computer software.
Replikin Analysis
[0080] Embodiments of the present invention may be employed not
only to identify and locate Replikin patterns in amino acid
sequences. Embodiments may also be used to discover and analyze
similarities in the structure of Replikin patterns occurring in
different proteins, or to analyze different Replikin patterns
occurring in the same protein over time. FIG. 10. for example, is a
table illustrating a Replikin "fixed scaffold" structure that was
preserved in a "Bird Flu" influenza virus over an 87 year period
from 1917 to 2004. Embodiments of the present invention may
assemble a number of discovered Replikin patterns in proteins,
including Replikin patterns discovered in variants of the same
protein. Along with each Replikin pattern, embodiments of the
present invention may also associate a date when each protein was
first identified. When directed by a researcher, an embodiment may
sort and display a plurality of selected Replikin patterns
according to content, date or other criteria, in order to reveal
substantially fixed amino acid structures that have been preserved
in Replikin patterns over time and which may be present in
different proteins as well as variants of the same protein.
Further, when directed by a researcher, an embodiment may employ,
known methods of pattern analysis to compare a plurality of
selected Replikin patterns in order to identify such fixed amino
acid structures automatically. As an example, in FIG. 10, the
illustrated Replikin patterns appear to demonstrate--in this
case--a relatively fixed scaffold structure of (usually) 29 amino
acids that begins with a pair of lysine residues (kk) at the amino
terminal, ends with a pair of histidine residues (hh) at the
carboxyl terminal, and contains a lysine residue in either position
8, 10 or 11. This conservation of scaffold structure over decades
permits synthetic vaccines to be prepared rapidly and
inexpensively. To synthesize such vaccines after a Replikin
scaffolding structure has been identified, a researcher may select
elements of that scaffolding structure that are conserved over time
and which are also present in a current variant of a protein. A
vaccine may then be prepared based on the selected elements from
the scaffolding structure. Because such vaccines are based on
conserved scaffolding structures, they may be effective for
multiple years and may also be developed well in advance of an
anticipated outbreak.
[0081] The discovery of Replikins themselves, as well as
embodiments of the present invention for identifying and locating
Replikin patterns, provides targets for the identification of
pathogens, as well as facilitates the development of anti-pathogen
therapies, including vaccines. In general, knowledge of and
identification of the Replikin family of peptides enables
development of effective therapies and vaccines for any organism
that harbors Replikins. Specifically, identification of Replikins
provides for the detection of viruses and virus vaccine
development, including the influenza virus. Further, identification
of Replikins also provides for the detection of other pathogens,
such as malaria, anthrax and small pox virus, in addition to
enabling the development of therapies and vaccines that target
Replikin structures. Additional examples provided by the
identification of Replikins include the detection of infectious
disease Replikins, cancer immune Replikins and structural protein
Replikins.
[0082] Embodiments of the present invention enable important
Replikin patterns of amino acids to be recognized, located and
analyzed in manners that are not found in the prior art. Using
prior art capabilities, researchers have been limited in by
existing techniques for describing sequences of amino acids.
Indeed, limitations of the prior art have in some ways dampened
research in this field, since heretofore it has not been possible
to specify sequences of amino acids that comprise non-linear
attributes. Until the development of the methods and embodiments of
the present invention, descriptions of amino acid sequences were
limited to linear sequences containing, at most, repetitive
substrings and logical constraints on substring content.
Embodiments of the present invention enable a new class of amino
acid sequences to be discovered, located and analyzed using tools
not found in the prior art. This new class of amino acids is
characterized by attributes such as specific amino acid
concentration and distance relationships between specific amino
acids. These attributes transcend simple contiguous ordering and
thus are not easily described, discovered or located by existing
methods known in the art.
[0083] The functionality of the foregoing embodiments may be
provided on various computer platforms executing program
instructions. One such platform 1100 is illustrated in the
simplified block diagram of FIG. 11. There, the platform 1100 is
shown as being populated by a processor 1160, which communicates
with a number of peripheral devices via a bus subsystem 1150. These
peripheral devices typically include a memory subsystem 1110, a
network interface subsystem 1170, and an input/output (I/O) unit
1180. The processor 1160 may be any of a plurality of conventional
processing systems, including microprocessors, digital signal
processors and field programmable logic arrays. In some
applications, it may be advantageous to provide multiple processors
(not shown) in the platform 1100. The processor(s) 1160 execute
program instructions stored in the memory subsystem 1110. The
memory subsystem 1110 may include any combination of conventional
memory circuits, including electrical, magnetic or optical memory
systems. As shown in FIG. 11, the memory system may include read
only memories 1120, random access memories 1130 and bulk storage
1140. Memory subsystem 1110 not only stores program instructions
representing the various methods described herein but also may
store the data items on which these methods operate. Network
interface subsystem 1170 may provide an interface to outside
networks, including an interface to communications network 1190
comprising, for example, the Internet. I/O unit 1180 would permit
communication with external devices, which are not shown.
[0084] Several embodiments of the present invention are
specifically illustrated and described herein. However, it will be
appreciated that modifications and variations of the present
invention are covered by the teachings of the present invention
without departing from the spirit and intended scope of the
invention. Additionally, the teachings of the present invention may
be adaptable to other sequence-recognizing problems that have
heretofore been addressed using sequential linear analyses limited
to the identification of specific sequences of component elements.
Sequence CWU 1
1
108110PRTHomo sapiens 1Met Tyr Arg Pro Asp Val Val Arg Ala Arg 1 5
10229PRTInfluenza virusMOD_RES(13)Variable amino acid 2Lys Lys Asn
Ser Ala Tyr Pro Thr Ile Lys Arg Ser Xaa Asn Asn Thr 1 5 10 15 Asn
His Glu Asp Leu Leu Val Leu Trp Gly Ile His His 20 25
3379PRTUnknown OrganismDescription of Unknown Organism Uknown
TVFV2E envelope protein 3Glu Leu Arg Leu Arg Tyr Cys Ala Pro Ala
Gly Phe Ala Leu Leu Lys 1 5 10 15 Cys Asn Asp Ala Asp Tyr Asp Gly
Phe Lys Thr Asn Cys Ser Asn Val 20 25 30 Ser Val Val His Cys Thr
Asn Leu Met Asn Thr Thr Val Thr Thr Gly 35 40 45 Leu Leu Leu Asn
Gly Ser Tyr Ser Glu Asn Arg Thr Gln Ile Trp Gln 50 55 60 Lys His
Arg Thr Ser Asn Asp Ser Ala Leu Ile Leu Leu Asn Lys His 65 70 75
80Tyr Asn Leu Thr Val Thr Cys Lys Arg Pro Gly Asn Lys Thr Val Leu
85 90 95 Pro Val Thr Ile Met Ala Gly Leu Val Phe His Ser Gln Lys
Tyr Asn 100 105 110 Leu Arg Leu Arg Gln Ala Trp Cys His Phe Pro Ser
Asn Trp Lys Gly 115 120 125 Ala Trp Lys Glu Val Lys Glu Glu Ile Val
Asn Leu Pro Lys Glu Arg 130 135 140 Tyr Arg Gly Thr Asn Asp Pro Lys
Arg Ile Phe Phe Gln Arg Gln Trp 145 150 155 160Gly Asp Pro Glu Thr
Ala Asn Leu Trp Phe Asn Cys His Gly Glu Phe 165 170 175 Phe Tyr Cys
Lys Met Asp Trp Phe Leu Asn Tyr Leu Asn Asn Leu Thr 180 185 190 Val
Asp Ala Asp His Asn Glu Cys Lys Asn Thr Ser Gly Thr Lys Ser 195 200
205 Gly Asn Lys Arg Ala Pro Gly Pro Cys Val Gln Arg Thr Tyr Val Ala
210 215 220 Cys His Ile Arg Ser Val Ile Ile Trp Leu Glu Thr Ile Ser
Lys Lys 225 230 235 240Thr Tyr Ala Pro Pro Arg Glu Gly His Leu Glu
Cys Thr Ser Thr Val 245 250 255 Thr Gly Met Thr Val Glu Leu Asn Tyr
Ile Pro Lys Asn Arg Thr Asn 260 265 270 Val Thr Leu Ser Pro Gln Ile
Glu Ser Ile Trp Ala Ala Glu Leu Asp 275 280 285 Arg Tyr Lys Leu Val
Glu Ile Thr Pro Ile Gly Phe Ala Pro Thr Glu 290 295 300 Val Arg Arg
Tyr Thr Gly Gly His Glu Arg Gln Lys Arg Val Pro Phe 305 310 315
320Val Xaa Xaa Xaa Xaa Xaa Xaa Xaa Xaa Xaa Xaa Xaa Xaa Xaa Xaa Xaa
325 330 335 Xaa Xaa Xaa Xaa Xaa Xaa Xaa Val Gln Ser Gln His Leu Leu
Ala Gly 340 345 350 Ile Leu Gln Gln Gln Lys Asn Leu Leu Ala Ala Val
Glu Ala Gln Gln 355 360 365 Gln Met Leu Lys Leu Thr Ile Trp Gly Val
Lys 370 375 4422PRTHomo sapiens 4Met Tyr Arg Pro Asp Val Val Arg
Ala Arg Lys Arg Val Cys Trp Glu 1 5 10 15 Pro Trp Val Ile Gly Leu
Val Ile Phe Ile Ser Leu Ile Val Leu Ala 20 25 30 Val Cys Ile Gly
Leu Thr Val His Tyr Val Arg Tyr Asn Gln Lys Lys 35 40 45 Thr Tyr
Asn Tyr Tyr Ser Thr Leu Ser Phe Thr Thr Asp Lys Leu Tyr 50 55 60
Ala Glu Phe Gly Arg Glu Ala Ser Asn Asn Phe Thr Glu Met Ser Gln 65
70 75 80Arg Leu Glu Ser Met Val Lys Asn Ala Phe Tyr Lys Ser Pro Leu
Arg 85 90 95 Glu Glu Phe Val Lys Ser Gln Val Ile Lys Phe Ser Gln
Gln Lys His 100 105 110 Gly Val Leu Ala His Met Leu Leu Ile Cys Arg
Phe His Ser Thr Glu 115 120 125 Asp Pro Glu Thr Val Asp Lys Ile Val
Gln Leu Val Leu His Glu Lys 130 135 140 Leu Gln Asp Ala Val Gly Pro
Pro Lys Val Asp Pro His Ser Val Lys 145 150 155 160Ile Lys Lys Ile
Asn Lys Thr Glu Thr Asp Ser Tyr Leu Asn His Cys 165 170 175 Cys Gly
Thr Arg Arg Ser Lys Thr Leu Gly Gln Ser Leu Arg Ile Val 180 185 190
Gly Gly Thr Glu Val Glu Glu Gly Glu Trp Pro Trp Gln Ala Ser Leu 195
200 205 Gln Trp Asp Gly Ser His Arg Cys Gly Ala Thr Leu Ile Asn Ala
Thr 210 215 220 Trp Leu Val Ser Ala Ala His Cys Phe Thr Thr Tyr Lys
Asn Pro Ala 225 230 235 240Arg Trp Thr Ala Ser Phe Gly Val Thr Ile
Lys Pro Ser Lys Met Lys 245 250 255 Arg Gly Leu Arg Arg Ile Ile Val
His Glu Lys Tyr Lys His Pro Ser 260 265 270 His Asp Tyr Asp Ile Ser
Leu Ala Glu Leu Ser Ser Pro Val Pro Tyr 275 280 285 Thr Asn Ala Val
His Arg Val Cys Leu Pro Asp Ala Ser Tyr Glu Phe 290 295 300 Gln Pro
Gly Asp Val Met Phe Val Thr Gly Phe Gly Ala Leu Lys Asn 305 310 315
320Asp Gly Tyr Ser Gln Asn His Leu Arg Gln Ala Gln Val Thr Leu Ile
325 330 335 Asp Ala Thr Thr Cys Asn Glu Pro Gln Ala Tyr Asn Asp Ala
Ile Thr 340 345 350 Pro Arg Met Leu Cys Ala Gly Ser Leu Glu Gly Lys
Thr Asp Ala Cys 355 360 365 Gln Gly Asp Ser Gly Gly Pro Leu Val Ser
Ser Asp Ala Arg Asp Ile 370 375 380 Trp Tyr Leu Ala Gly Ile Val Ser
Trp Gly Asp Glu Cys Ala Lys Pro 385 390 395 400Asn Lys Pro Gly Val
Tyr Thr Arg Val Thr Ala Leu Arg Asp Trp Ile 405 410 415 Thr Ser Lys
Thr Gly Ile 420 529PRTInfluenza virus 5Lys Lys Gly Thr Ser Tyr Pro
Lys Leu Ser Lys Ser Tyr Thr Asn Asn 1 5 10 15 Lys Gly Lys Glu Val
Leu Val Leu Trp Gly Val His His 20 25 629PRTInfluenza virus 6Lys
Lys Gly Ser Ser Tyr Pro Lys Leu Ser Lys Ser Tyr Val Asn Asn 1 5 10
15 Lys Gly Lys Glu Val Leu Val Leu Trp Gly Val His His 20 25
729PRTInfluenza virus 7Lys Lys Glu Asn Ser Tyr Pro Lys Leu Ser Lys
Ser Tyr Val Asn Asn 1 5 10 15 Lys Gly Lys Glu Val Leu Val Leu Trp
Gly Val His His 20 25 829PRTInfluenza virus 8Lys Lys Gly Asp Ser
Tyr Pro Lys Leu Thr Asn Ser Tyr Val Asn Asn 1 5 10 15 Lys Gly Lys
Glu Val Leu Val Leu Trp Gly Val His His 20 25 929PRTInfluenza virus
9Lys Lys Gly Thr Ser Tyr Pro Lys Leu Ser Lys Ser Tyr Thr Asn Asn 1
5 10 15 Lys Gly Lys Glu Val Leu Val Leu Trp Gly Val His His 20 25
109PRTMycoplasma pulmonis 10Lys Lys Glu Lys Thr Thr His Asn Lys 1 5
1129PRTInfluenza virus 11Lys Lys Gly Thr Ser Tyr Pro Lys Leu Ser
Lys Ser Tyr Thr Asn Asn 1 5 10 15 Lys Gly Lys Glu Val Leu Val Leu
Trp Gly Val His His 20 25 1229PRTInfluenza virus 12Lys Lys Gly Asn
Ser Tyr Pro Lys Leu Ser Lys Ser Tyr Thr Asn Asn 1 5 10 15 Lys Gly
Lys Glu Val Leu Val Ile Trp Gly Val His His 20 25 1329PRTInfluenza
virus 13Lys Lys Gly Asn Ser Tyr Pro Lys Leu Ser Lys Ser Tyr Thr Asn
Asn 1 5 10 15 Lys Gly Lys Glu Val Leu Val Ile Trp Gly Val His His
20 25 1429PRTInfluenza virus 14Lys Lys Gly Thr Ser Tyr Pro Lys Leu
Ser Lys Ser Tyr Thr Asn Asn 1 5 10 15 Lys Gly Lys Glu Val Leu Val
Leu Trp Gly Val His His 20 25 1529PRTInfluenza virus 15Lys Lys Gly
Asn Ser Tyr Pro Lys Leu Ser Lys Ser Tyr Thr Asn Asn 1 5 10 15 Lys
Gly Lys Glu Val Leu Val Ile Trp Gly Val His His 20 25
1629PRTInfluenza virus 16Lys Lys Gly Thr Ser Tyr Pro Lys Leu Ser
Lys Ser Tyr Thr Asn Asn 1 5 10 15 Lys Gly Lys Glu Val Leu Val Leu
Trp Gly Val His His 20 25 1729PRTInfluenza virus 17Lys Lys Gly Thr
Ser Tyr Pro Lys Leu Ser Lys Ser Tyr Thr Asn Asn 1 5 10 15 Lys Gly
Lys Glu Val Leu Val Leu Trp Gly Val His His 20 25 1813PRTHepatitis
C virus 18His Tyr Pro Pro Lys Pro Gly Cys Ile Val Pro Ala Lys 1 5
10 1929PRTInfluenza virus 19Lys Lys Gly Asn Ser Tyr Pro Lys Leu Ser
Lys Ser Tyr Thr Asn Asn 1 5 10 15 Lys Gly Lys Glu Val Leu Val Ile
Trp Gly Val His His 20 25 2029PRTInfluenza virus 20Lys Lys Gly Asn
Ser Tyr Pro Lys Leu Ser Lys Ser Tyr Thr Asn Asn 1 5 10 15 Lys Gly
Lys Glu Val Leu Val Ile Trp Gly Val His His 20 25 2129PRTInfluenza
virus 21Lys Lys Gly Asn Ser Tyr Pro Lys Leu Ser Lys Ser Tyr Thr Asn
Asn 1 5 10 15 Lys Gly Lys Glu Val Leu Val Ile Trp Gly Val His His
20 25 2229PRTInfluenza virus 22Lys Lys Gly Asp Ser Tyr Pro Lys Leu
Ser Lys Ser Tyr Thr Asn Asn 1 5 10 15 Lys Gly Lys Glu Val Leu Val
Ile Trp Gly Val His His 20 25 2329PRTInfluenza virus 23Lys Lys Gly
Ser Ser Tyr Pro Lys Leu Ser Lys Ser Tyr Val Asn Asn 1 5 10 15 Lys
Gly Lys Glu Val Leu Val Leu Trp Gly Val His His 20 25
2429PRTInfluenza virus 24Lys Lys Gly Ser Ser Tyr Pro Lys Leu Ser
Lys Ser Tyr Val Asn Asn 1 5 10 15 Lys Gly Lys Glu Val Leu Val Leu
Trp Gly Val His His 20 25 2529PRTInfluenza virus 25Lys Lys Gly Asn
Ser Tyr Pro Lys Leu Ser Lys Ser Tyr Thr Asn Asn 1 5 10 15 Lys Gly
Lys Glu Val Leu Val Ile Trp Gly Val His His 20 25 2629PRTInfluenza
virus 26Lys Lys Gly Asn Ser Tyr Pro Lys Leu Ser Lys Ser Tyr Thr Asn
Asn 1 5 10 15 Lys Gly Lys Glu Val Leu Val Ile Trp Gly Val His His
20 25 2729PRTInfluenza virus 27Lys Lys Gly Asn Ser Tyr Pro Lys Leu
Ser Lys Ser Tyr Thr Asn Asn 1 5 10 15 Lys Gly Lys Glu Val Leu Val
Ile Trp Gly Val His His 20 25 2829PRTInfluenza virus 28Lys Lys Gly
Asn Ser Tyr Pro Lys Leu Ser Lys Ser Tyr Thr Asn Asn 1 5 10 15 Lys
Gly Lys Glu Val Leu Val Ile Trp Gly Val His His 20 25
2929PRTInfluenza virus 29Lys Lys Gly Asn Ser Tyr Pro Lys Ile Ser
Lys Ser Tyr Ile Asn Asn 1 5 10 15 Lys Glu Lys Glu Val Leu Val Leu
Trp Gly Ile His His 20 25 3029PRTInfluenza virus 30Lys Lys Gly Asn
Ser Tyr Pro Lys Leu Ser Lys Ser Tyr Ile Asn Asn 1 5 10 15 Lys Lys
Lys Glu Val Leu Val Ile Trp Gly Ile His His 20 25 3129PRTInfluenza
virus 31Lys Lys Gly Asn Ser Tyr Pro Lys Leu Ser Lys Ser Tyr Ile Asn
Asn 1 5 10 15 Lys Gly Lys Lys Val Leu Val Leu Trp Gly Ile His His
20 25 3229PRTInfluenza virus 32Lys Lys Gly Thr Ser Tyr Pro Lys Leu
Ser Lys Ser Tyr Thr Asn Asn 1 5 10 15 Lys Lys Lys Glu Val Leu Val
Leu Trp Gly Val His His 20 25 3328PRTInfluenza virus 33Lys Asn Gly
Leu Tyr Pro Asn Leu Ser Lys Ser Tyr Ala Asn Asn Lys 1 5 10 15 Glu
Lys Glu Val Leu Val Leu Trp Gly Val His His 20 25 3428PRTInfluenza
virus 34Lys Asn Gly Leu Tyr Pro Asn Leu Ser Lys Ser Tyr Ala Asn Asn
Lys 1 5 10 15 Glu Lys Glu Val Leu Ile Leu Trp Gly Val His His 20 25
3529PRTInfluenza virus 35Lys Lys Glu Asn Ser Tyr Pro Lys Leu Arg
Lys Ser Ile Ile Ile Asn 1 5 10 15 Lys Lys Glu Val Lys Leu Val Ile
Trp Gly Ile His His 20 25 3619PRTInfluenza virus 36Lys Ser Tyr Lys
Asn Thr Arg Lys Asp Pro Ala Leu Ile Ile Trp Gly 1 5 10 15 Ile His
His 3729PRTInfluenza virus 37Lys Lys Gly Pro Asn Tyr Pro Val Ala
Lys Arg Ser Tyr Asn Asn Thr 1 5 10 15 Ser Gly Glu Gln Met Leu Ile
Ile Trp Gly Val His His 20 25 3829PRTInfluenza virus 38Lys Lys Gly
Pro Asn Tyr Pro Val Ala Lys Arg Ser Tyr Asn Asn Thr 1 5 10 15 Ser
Gly Glu Gln Met Leu Ile Ile Trp Gly Ile His His 20 25
3929PRTInfluenza virus 39Lys Lys Asn Asn Ala Tyr Pro Thr Ile Lys
Arg Thr Tyr Asn Asn Thr 1 5 10 15 Asn Val Glu Asp Leu Leu Ile Leu
Trp Gly Ile His His 20 25 4029PRTInfluenza virus 40Lys Lys Asn Asn
Ala Tyr Pro Thr Ile Lys Arg Ser Tyr Ser Asn Thr 1 5 10 15 Asn Gln
Glu Asp Leu Leu Val Leu Trp Gly Ile His His 20 25 4129PRTInfluenza
virus 41Lys Lys Asn Asn Ala Tyr Pro Thr Ile Lys Arg Thr Tyr Asn Asn
Thr 1 5 10 15 Asn Ile Glu Asp Leu Leu Ile Leu Trp Gly Ile His His
20 25 4229PRTInfluenza virus 42Lys Lys Asn Asn Ala Tyr Pro Thr Ile
Lys Arg Thr Tyr Asn Asn Thr 1 5 10 15 Asn Met Glu Asp Leu Leu Ile
Leu Trp Gly Ile His His 20 25 439PRTUnknown OrganismDescription of
Unknown Organism Unknown macrophage infectivity potentiator peptide
43Lys Val His Phe Phe Gln Leu Lys Lys 1 5 4429PRTInfluenza virus
44Lys Lys Gly Asn Ala Tyr Pro Thr Ile Lys Arg Thr Tyr Asn Asn Thr 1
5 10 15 Asn Val Glu Asp Leu Leu Ile Leu Trp Gly Ile His His 20 25
4529PRTInfluenza virus 45Lys Lys Asn Asn Thr Tyr Pro Thr Ile Lys
Arg Ser Tyr Asn Asn Thr 1 5 10 15 Asn Gln Glu Asp Leu Leu Ile Leu
Trp Gly Ile His His 20 25 4629PRTInfluenza virus 46Lys Lys Asn Ser
Ala Tyr Pro Thr Ile Lys Arg Ser Tyr Asn Asn Thr 1 5 10 15 Asn Gln
Glu Asp Leu Leu Val Leu Trp Gly Ile His His 20 25 4729PRTInfluenza
virus 47Lys Lys Asn Ser Ala Tyr Pro Thr Ile Lys Arg Ser Tyr Asn Asn
Thr 1 5 10 15 Asn Gln Glu Asp Leu Leu Val Leu Trp Gly Ile His His
20 25 487PRTRous sarcoma virus 48Lys Lys Leu Arg His Glu Lys 1 5
497PRTAvian sarcoma virus 49Lys Lys Leu Arg His Asp Lys 1
5 507PRTUnknown OrganismDescription of Unknown Organism Unknown
c-yes, colon cancer peptide 50Lys Lys Leu Arg His Asp Lys 1 5
517PRTAvian sarcoma virus 51Lys Lys Leu Arg His Glu Lys 1 5
527PRTHomo sapiens 52Lys Lys Leu Arg His Glu Lys 1 5 538PRTUnknown
OrganismDescription of Unknown Organism Unknown neuroblastoma
oncogene peptide 53Lys Gln Ala His Glu Leu Ala Lys 1 5
548PRTPolyamavirus sp. 54Lys Thr His Arg Phe Ser Lys His 1 5
558PRTSindbis virus 55Lys Asn Leu His Glu Lys Ile Lys 1 5
569PRTHuman papilloamavirus type 71 56Lys His Arg Pro Leu Leu Gln
Leu Lys 1 5 577PRTUnknown OrganismDescription of Unknown Organism
Unknown v-erbB tumor virus peptide 57Lys Ser Pro Asn His Val Lys 1
5 588PRTFeline sarcoma virus 58Lys Asn Ile His Leu Glu Lys Lys 1 5
598PRTUnknown OrganismDescription of Unknown Organism Unknown c-fms
myelomonocytic tumor peptide 59Lys Asn Ile His Leu Glu Lys Lys 1 5
6010PRTPolyamavirus sp. 60Lys Pro His Leu Ala Gln Ser Leu Glu Lys 1
5 10619PRTPolyamavirus sp. 61Lys Gln His Arg Glu Leu Lys Asp Lys 1
5 629PRTPolyamavirus sp. 62Lys Gln His Arg Glu Leu Lys Asp Lys 1 5
6312PRTMurine leukemia virus 63Lys Val Pro Val Leu Ile Ser Pro Thr
Leu Lys His 1 5 10 6413PRTHuman T-cell lymphotropic virus 64Lys Ser
Leu Leu Leu Glu Val Asp Lys Asp Ile Ser His 1 5 10 6513PRTUnknown
OrganismDescription of Unknown Organism Unknown c-kit, GI tumor
peptide 65Lys Ala Gly Ile Thr Ile Met Val Lys Arg Glu Tyr His 1 5
10 668PRTUnknown OrganismDescription of Unknown Organism Unknown
transforming protein myb 66Lys Ser Gly Lys His Leu Gly Lys 1 5
679PRTUnknown OrganismDescription of Unknown Organism Unknown
transforming protein myc 67Lys Arg Arg Glu Gln Leu Lys His Lys 1 5
6810PRTUnknown OrganismDescription of Unknown Organism Unknown
Ras-related GTP-binding protein 68Lys Ser Phe Glu Val Ile Lys Val
Ile His 1 5 10698PRTUnknown OrganismDescription of Unknown Organism
Unknown transforming protein ras (teratocarcinoma) 69Lys Lys Lys
His Thr Val Lys Lys 1 5 709PRTUnknown OrganismDescription of
Unknown Organism Unknown TRAF-associated NFkB activator peptide
70Lys Ala Gln Lys Asp His Leu Ser Lys 1 5 7110PRTUnknown
OrganismDescription of Unknown Organism Unknown RFP transforming
protein 71His Leu Lys Arg Val Lys Asp Leu Lys Lys 1 5
107211PRTUnknown OrganismDescription of Unknown Organism Unknown
transforming protein 72Lys Tyr Gly Ser Pro Lys His Arg Leu Ile Lys
1 5 10 7313PRTPapilloma virus type 11 73Lys Leu Lys His Ile Leu Gly
Lys Ala Arg Phe Ile Lys 1 5 10 7412PRTUnknown OrganismDescription
of Unknown Organism Unknown tyrosine kinasc protein 74Lys Gly Asp
His Val Lys His Tyr Lys Ile Arg Lys 1 5 10 7513PRTUnknown
OrganismDescription of Unknown Organism Unknown transforming
protein 75Lys Glu Lys Leu Arg Asp Val Met Val Asp Arg His Lys 1 5
10 7615PRTUnknown OrganismDescription of Unknown Organism Unknown
transforming protein 76Lys Leu Gln Ala Arg Gln Gln Gln Leu Leu Lys
Lys Ile Glu His 1 5 10 157714PRTUnknown OrganismDescription of
Unknown Organism Unknown fibroblast growth factor 4 peptide 77Lys
Lys Gly Asn Arg Val Ser Pro Thr Met Lys Val Thr His 1 5 10
789PRTUnknown OrganismDescription of Unknown Organism Unknown
Matrix metalloproteinase 7 peptide 78Lys Glu Ile Pro Leu His Phe
Arg Lys 1 5 798PRTUnknown OrganismDescription of Unknown Organism
Unknown transcription factor 7-like peptide 79Lys Lys Lys Pro His
Ile Lys Lys 1 5 809PRTUnknown OrganismDescription of Unknown
Organism Unknown breast cancer antigen peptide 80Lys Thr Arg His
Asp Pro Leu Ala Lys 1 5 8110PRTUnknown OrganismDescription of
Unknown Organism Unknown BRCA-1-Associated protein 81Lys His His
Pro Lys Asp Asn Leu Ile Lys 1 5 108210PRTUnknown
OrganismDescription of Unknown Organism Unknown autoantigen peptide
82Lys His Lys Arg Lys Lys Phe Arg Gln Lys 1 5 108310PRTUnknown
OrganismDescription of Unknown Organism Unknown Glioma Replikin
peptide 83Lys Ala Gly Val Ala Phe Leu His Lys Lys 1 5
108410PRTUnknown OrganismDescription of Unknown Organism Unknown
ovarian cancer antigen peptide 84Lys His Lys Arg Lys Lys Phe Arg
Gln Lys 1 5 108510PRTUnknown OrganismDescription of Unknown
Organism Unknown EE L leukemia peptide 85Lys Lys Lys Ser Lys Lys
His Lys Asp Lys 1 5 108611PRTUnknown OrganismDescription of Unknown
Organism Unknown Poto-oncogene peptide 86His Lys Ser Glu Lys Pro
Ala Leu Pro Arg Lys 1 5 10 8714PRTUnknown OrganismDescription of
Unknown Organism Unknown adenomatosis polyposis coli peptide 87Lys
Lys Lys Lys Pro Ser Arg Leu Lys Gly Asp Asn Glu Lys 1 5 10
8816PRTUnknown OrganismDescription of Unknown Organism Unknown
gastric cancer transforming protein 88Lys Thr Lys Lys Gly Asn Arg
Val Ser Pro Thr Met Lys Val Thr His 1 5 10 15 8918PRTUnknown
OrganismDescription of Unknown Organism Unknown K-RAS 2B
transforming protein 89Lys His Lys Glu Lys Met Ser Lys Asp Gly Lys
Lys Lys Lys Lys Lys 1 5 10 15 Ser Lys 9029PRTInfluenza virus 90Lys
Lys Asn Ser Ala Tyr Pro Thr Ile Lys Arg Ser Tyr Asn Asn Thr 1 5 10
15 Asn Gln Glu Asp Leu Leu Val Leu Trp Gly Ile His His 20 25
9129PRTInfluenza virus 91Lys Lys Asn Ser Ala Tyr Pro Thr Ile Lys
Arg Ser Tyr Asn Asn Thr 1 5 10 15 Asn Gln Glu Asp Leu Leu Val Leu
Trp Gly Ile His His 20 25 9229PRTInfluenza virus 92Lys Lys Asn Ser
Ala Tyr Pro Thr Ile Lys Arg Ser Tyr Asn Asn Thr 1 5 10 15 Asn Gln
Glu Asp Leu Leu Val Leu Trp Gly Ile His His 20 25 9329PRTInfluenza
virus 93Lys Lys Asn Ser Ala Tyr Pro Thr Ile Lys Arg Ser Tyr Asn Asn
Thr 1 5 10 15 Asn Gln Glu Asp Leu Leu Val Leu Trp Gly Ile His His
20 25 9429PRTInfluenza virus 94Lys Lys Asn Asn Ala Tyr Pro Thr Ile
Lys Arg Ser Tyr Asn Asn Thr 1 5 10 15 Asn Gln Glu Asp Leu Leu Val
Leu Trp Gly Ile His His 20 25 9529PRTInfluenza virus 95Lys Lys Asn
Ser Ala Tyr Pro Thr Ile Lys Arg Ser Tyr Asn Asn Thr 1 5 10 15 Asn
Gln Glu Asp Leu Leu Val Leu Trp Gly Ile His His 20 25
9629PRTInfluenza virus 96Lys Lys Asn Ser Thr Tyr Pro Thr Ile Lys
Arg Ser Tyr Asn Asn Thr 1 5 10 15 Asn Gln Glu Asp Leu Leu Val Leu
Trp Gly Ile His His 20 25 9729PRTInfluenza virus 97Lys Lys Asn Ser
Thr Tyr Pro Thr Ile Lys Arg Ser Tyr Asn Asn Thr 1 5 10 15 Asn Gln
Glu Asp Leu Leu Val Leu Trp Gly Ile His His 20 25 9829PRTInfluenza
virus 98Lys Lys Asn Ser Thr Tyr Pro Thr Ile Lys Arg Ser Tyr Asn Asn
Thr 1 5 10 15 Asn Gln Glu Asp Leu Leu Val Leu Trp Gly Ile His His
20 25 9929PRTInfluenza virus 99Lys Lys Asn Ser Thr Tyr Pro Thr Ile
Lys Arg Ser Tyr Asn Asn Thr 1 5 10 15 Asn Gln Glu Asp Leu Leu Val
Leu Trp Gly Ile His His 20 25 10029PRTInfluenza virus 100Lys Lys
Asn Ser Thr Tyr Pro Thr Ile Lys Arg Ser Tyr Asn Asn Thr 1 5 10 15
Asn Gln Glu Asp Leu Leu Val Leu Trp Gly Ile His His 20 25
10129PRTInfluenza virus 101Lys Lys Asn Asn Ala Tyr Pro Thr Ile Lys
Arg Ser Tyr Asn Asn Thr 1 5 10 15 Asn Gln Glu Asp Leu Leu Val Leu
Trp Gly Ile His His 20 25 10229PRTInfluenza virus 102Lys Lys Asn
Ser Thr Tyr Pro Thr Ile Lys Arg Ser Tyr Asn Asn Thr 1 5 10 15 Asn
Gln Glu Asp Leu Leu Val Met Trp Gly Ile His His 20 25
10329PRTInfluenza virus 103Lys Lys Asn Ser Ala Tyr Pro Thr Ile Lys
Arg Ser Tyr Asn Asn Thr 1 5 10 15 Asn Gln Glu Asp Leu Leu Val Leu
Trp Gly Ile His His 20 25 10429PRTInfluenza virus 104Lys Lys Asn
Ser Thr Tyr Pro Thr Ile Lys Arg Ser Tyr Asn Asn Thr 1 5 10 15 Asn
Gln Glu Asp Leu Leu Val Leu Trp Gly Ile His His 20 25
10529PRTInfluenza virus 105Lys Lys Asn Ser Thr Tyr Pro Thr Ile Lys
Arg Ser Tyr Asn Asn Thr 1 5 10 15 Asn Gln Glu Asp Leu Leu Val Leu
Trp Gly Ile His His 20 25 10629PRTInfluenza virus 106Lys Lys Asn
Ser Thr Tyr Pro Thr Ile Lys Arg Ser Tyr Asn Asn Thr 1 5 10 15 Asn
Gln Glu Asp Leu Leu Val Leu Trp Gly Ile Gln His 20 25
10729PRTInfluenza virus 107Lys Lys Asn Ser Ala Tyr Pro Ile Ile Lys
Arg Ser Tyr Asn Asn Thr 1 5 10 15 Asn Gln Glu Asp Leu Leu Val Leu
Trp Gly Ile His His 20 25 1084PRTArtificial SequenceDescription of
Artificial Sequence Synthetic peptide 108Met Asp Glu Leu1
* * * * *