Search
Search for Sequences
For all types of sequence searches:
- Do not enter spaces or dashes.
Example: do not use: G E T R A P L, G-E-T-R-A-P-L - Do not enter amino acid modifications, phosphorylation, terminal and other marks.
Example: do not use: Myr-GE(pT)RAPL-NH2 - Remove the D prefix from D-amino acids.
Example: do not use: Gly-Glu-Thr-Arg-D-Ala-Pro-Leu - Do not use three letter amino acid code, or full names.
Example: do not use: Gly-Glu-Thr-Arg-Ala-Pro-Leu - Use only single letter amino acid code, uppercase or lowercase.
Example: for all of the above, use: GETRAPL, getrapl
To search for sequences, use the tools designed specifically for this purpose. In most cases, these are not Quick Search or Advanced Search, which should be used for text search or pattern/motif search. Instead, we suggest to use BLAST search (if the query sequence is 4 amino acids or longer) or Smith-Waterman search (3 amino acids or longer). For shorter sequences, use either of these, but increase Expect or E(). BLAST search and Smith-Waterman search:
- use substitution matrices which take into account different similarities or distances between amino acids. For example, when searching for GETRAPL, the hit GETKAPL will be closer to the top than GETDAPL. This is based on the fact that R is more often replaced with K than with D in evolution. In most cases this is what you want.
- allow multiple query sequences in a single search (bulk queries).
- find partial or shorter matches, in addition to exact matches. Although we store only peptides that are 20 amino acids or shorter, the query can be much longer.
Try this query example:
>exact_query GETRAPL >partial_query GETKAPL >long_query GETRAPLAQAQAQAQAQAQAQAQAQAQAQAQAQAQAQAQAQAQAQAQ AQAQAQAQAQAQAQAQAQAQAQAQAQAQAQAQAQAQAQAQAQAQAQA QAQAQAQAQAQAQAQAQAQAQAQAQAQAQAQAQAQAQAQAQAQAQAQ AQAQAQAQAQ
As the next best choice, use Advanced Search for Peptide: Sequence, or Quick Search. Note that a partially matching (GETKAPL) or a long (GETRAPLAQAQ...) query will not return any results. This is probably not what you want. Quick Search and Advanced Search are used mostly for text, rather than sequence, search. Their main advantage for sequence search is the possibility to search for certain more precisely specified patterns or motifs. Examples:
- GET*APL will find entries with GET and APL having 0 or more characters in between, such as GETAPL, GETRAPL, GETKAPL, AAAGETQQAPLQQ, etc.
Beware that Quick Search will also find strings like this in text: 'GET me an APL', because it searches all fields: sequences, text, and all. - G_T_APL will find entries with G followed by any one character, followed by T, followed by any one character, followed by APL - such as GETRAPL, GQTAAPL, KKGQTAAPLWW, etc.
Quick and Advanced Search
For both Quick Search and Advanced Search, queries are case-insensitive.
The wild-card characters are star - '*' and underscore - '_'. Star matches zero or more characters. Underscore matches any single character. Star is automatically added to the left and to the right of the query. To prevent this, put double quotes around the query. To browse the entries, click on 'Browse Interactions', or use Quick Search with an empty query or with * and hit 'submit'.
Examples below show whether the entry can be found with the search query.
| Entry | Search query | Found? |
|---|---|---|
| abc | abc | yes |
| abc | AbC | yes |
| abc | "abc" | yes |
| abc de | abc | yes |
| abc de | "abc" | no |
| abc de | bc d | yes |
| abc de | bc * | yes |
| abc de | bc | yes |
| abc de | ab * | no |
| abc de | b*d | yes |
| abc de | d*b | no |
| abc de | "abc de" | yes |
| abc de | "a*d*" | yes |
| abc de | "a_c*" | yes |
Boolean queries (AND, OR, NOT) are not supported. Examples:
- Do not use: MMP and Cathepsin
- Use: MMP
- Use: MMP*Cathepsin
- Use: Cathepsin*MMP
We store MEDLINE abstracts without additional modifications, and do not resolve gene synonyms. Thus, queries for MMP2 and MMP-2 are not the same (just as they are not the same in MEDLINE/PubMed).
Got fewer results than expected? Try using a less restrictive query. Examples:
- MMP2 (most restrictive)
- MMP*2
- MMP (least restrictive)
- Thromboembolism (most restrictive)
- Thromboemb
- Thrombo
- Thromb (least restrictive)
Quick Search
Quick Search searches all text fields.
Advanced Search
Advanced Search searches individual fields. Using only * without other characters is not allowed, unlike in Quick Search. The query fields are automatically connected by 'AND'.
Examples:
- To find entries with score 0.9 exactly, use query: score: 0.9
- To find entries manually marked as valid peptide sequence, use query: score: > 0.6
- To find entries where the interaction takes place in human cells or tissues, use query: organism: Homo sapiens, or organism: sapiens, for short.
- To find entries that have peptide motif 'RGD' and the word 'integrin' in the abstract text, use query: sequence: RGD, text: integrin
- To find entries with Pubmed id 14759804, use query: text id: 14759804
BLAST Search
BLAST search uses NCBI blastall program. BLAST is a faster but less accurate method than Smith-Waterman search. The default option settings are optimized for peptide database: -p blastp -W 2 -F F -T T .
They can be overridden using 'Other advanced options'. For example, to search with the options similar to the options suggested by NCBI for short, nearly exact matches, use Matrix: PAM30, Expect: 10000, other advanced options: -G 9 -E 1. The full list of available blastall options is below. See more info on the NCBI BLAST web page.
-p Program Name [String]
-e Expectation value (E) [Real]
default = 10.0
-m alignment view options:
0 = pairwise,
1 = query-anchored showing identities,
2 = query-anchored no identities,
3 = flat query-anchored, show identities,
4 = flat query-anchored, no identities,
5 = query-anchored no identities and blunt ends,
6 = flat query-anchored, no identities and blunt ends,
7 = XML Blast output,
8 = tabular,
9 tabular with comment lines
10 ASN, text
11 ASN, binary [Integer]
default = 0
-F Filter query sequence (DUST with blastn, SEG with others) [String]
default = T
-G Cost to open a gap (zero invokes default behavior) [Integer]
default = 0
-E Cost to extend a gap (zero invokes default behavior) [Integer]
default = 0
-X X dropoff value for gapped alignment (in bits) (zero invokes default behavior)
blastn 30, megablast 20, tblastx 0, all others 15 [Integer]
default = 0
-I Show GI's in deflines [T/F]
default = F
-q Penalty for a nucleotide mismatch (blastn only) [Integer]
default = -3
-r Reward for a nucleotide match (blastn only) [Integer]
default = 1
-v Number of database sequences to show one-line descriptions for (V) [Integer]
default = 500
-b Number of database sequence to show alignments for (B) [Integer]
default = 250
-f Threshold for extending hits, default if zero
blastp 11, blastn 0, blastx 12, tblastn 13
tblastx 13, megablast 0 [Integer]
default = 0
-g Perform gapped alignment (not available with tblastx) [T/F]
default = T
-Q Query Genetic code to use [Integer]
default = 1
-D DB Genetic code (for tblast[nx] only) [Integer]
default = 1
-a Number of processors to use [Integer]
default = 1
-O SeqAlign file [File Out] Optional
-J Believe the query defline [T/F]
default = F
-M Matrix [String]
default = BLOSUM62
-W Word size, default if zero (blastn 11, megablast 28, all others 3) [Integer]
default = 0
-z Effective length of the database (use zero for the real size) [Real]
default = 0
-K Number of best hits from a region to keep (off by default, if used a value of 100
is recommended) [Integer]
default = 0
-P 0 for multiple hit, 1 for single hit (does not apply to blastn) [Integer]
default = 0
-Y Effective length of the search space (use zero for the real size) [Real]
default = 0
-S Query strands to search against database (for blast[nx], and tblastx)
3 is both, 1 is top, 2 is bottom [Integer]
default = 3
-T Produce HTML output [T/F]
default = F
-l Restrict search of database to list of GI's [String] Optional
-U Use lower case filtering of FASTA sequence [T/F] Optional
-y X dropoff value for ungapped extensions in bits (0.0 invokes default behavior)
blastn 20, megablast 10, all others 7 [Real]
default = 0.0
-Z X dropoff value for final gapped alignment in bits (0.0 invokes default behavior)
blastn/megablast 50, tblastx 0, all others 25 [Integer]
default = 0
-R PSI-TBLASTN checkpoint file [File In] Optional
-n MegaBlast search [T/F]
default = F
-L Location on query sequence [String] Optional
-A Multiple Hits window size, default if zero (blastn/megablast 0, all others 40 [Integer]
default = 0
-w Frame shift penalty (OOF algorithm for blastx) [Integer]
default = 0
-t Length of the largest intron allowed in a translated nucleotide sequence when linking
multiple distinct alignments. (0 invokes default behavior; a negative value disables
linking.) [Integer]
default = 0
-B Number of concatenated queries, for blastn and tblastn [Integer] Optional
default = 0
Smith-Waterman Search
Smith-Waterman search uses SSEARCH program. Smith-Waterman search is a more accurate, but slower method than BLAST. The default option settings are optimized for peptide database: -w 80 -z 2 -L -m 6 -H -Q .
They can be overridden using 'Other advanced options'. For example, to search with Penalty for the first residue in a gap = -6, use: -f 6. The full list of available FASTA/SSEARCH options is below (use SSEARCH options only).
-a (fasta3, ssearch3 only) show both sequences in their
entirety.
-A force Smith-Waterman alignments for fasta3 DNA sequences.
By default, only fasta3 protein sequence comparisons use
Smith-Waterman alignments.
-B Show normalized score as a z-score, rather than a bit-score
in the list of best scores.
-b # Number of sequence scores to be shown on output. In the
absence of this option, fasta (and tfasta and ssearch)
display all library sequences obtaining similarity scores
with expectations less than 10.0 if optimized score are
used, or 2.0 if they are not. The -b option can limit the
display further, but it will not cause additional sequences
to be displayed.
-c # Threshold score for optimization (OPTCUT). Set "-c 1" to
optimize every sequence in a database.
-E # Limit the number of scores and alignments shown based on the
expected number of scores. Used to override the expectation
value of 10.0 used by default. When used with -Q, -E 2.0
will show all library sequences with scores with an
expectation value <= 2.0.
-d # Maximum number of alignments to be displayed. Ignored if
"-Q" is not used.
-f Penalty for the first residue in a gap (-12 by default for
proteins, -16 for DNA, -15 for FAST[XY]/TFAST[XY]).
-F # Limit the number of scores and alignments shown based on the
expected number of scores. "-E #" sets the highest E()-value
shown; "-F #" sets the lowest E()-value. Thus, "-F 0.0001"
will not show any matches or alignments with E() < 0.0001.
This allows one to skip over close relationships in searches
for more distant relationships.
-g Penalty for additional residues in a gap (-2 by default for
proteins, -4 for DNA, -3 for FAST[XY]/TFAST[XY]).
-h Penalty for frameshift (fastx3/y3, tfastx3/y3 only).
-H Omit histogram.
-i Invert (reverse complement) the query sequence if it is DNA.
For tfasta3/x3/y3, search the reverse complement of the
library sequence only.
-j # Penalty for frameshift within a codon (fasty3/tfasty3 only).
-l file
Location of library menu file (FASTLIBS).
-L Display more information about the library sequence in the
alignment.
-M low-high
Range of amino acid sequence lengths to be included in the
search.
-m # Specify alignment type: 0, 1, 2, 3, 4, 5, 6, 9, 10
-m 0 -m 1 -m 2 -m 3 -m 4
MWRTCGPPYT MWRTCGPPYT MWRTCGPPYT MWRTCGPPYT
::..:: ::: xx X ..KS..Y... MWKSCGYPYT ----------
MWKSCGYPYT MWKSCGYPYT
-m 5 provides a combination of -m 4 and -m 0. -m 6 provides
-m 5 plus HTML formatting.
-m 9 provides coordinates and scores with the best score
information. A simple -m 9 extends the normal best score
information:
The best scores are: opt bits E(14548)
XURTG4 glutathione transferase (EC 2.5.1.18) 4 - ( 219) 1248 291.7 1.1e-79
to include the additional information (on the same line,
separated by a <tab>):
%_id %_gid sw alen an0 ax0 pn0 px0 an1 ax1 pn1 px1 gapq gapl fs
0.771 0.771 1248 218 1 218 1 218 1 218 1 219 0 0 0
-m 9c provides additional information: an encoded alignment
string. Thus:
10 20 30 40 50 60 70
GT8.7 NVRGLTHPIRMLLEYTDSSYDEKRYTMGDAPDFDRSQWLNEKFKL--GLDFPNLPYL-IDGSHKITQ
:.:: . :: :: . .::: : .: ::.: .: : ..:.. ::: :..:
XURTG NARGRMECIRWLLAAAGVEFDEK---------FIQSPEDLEKLKKDGNLMFDQVPMVEIDG-MKLAQ
20 30 40 50 60
would be encoded:
=23+9=13-2=10-1=3+1=5
The alignment encoding is with repect to the alignment, not
the sequences. The coordinate of the alignment is given
earlier in the " -m 9c" line.
-m 10
-m 10 is a new, parseable format for use with other
programs. See the file "readme.v20u4" for a more complete
description.
As of version "fa34t23b2", it has become possible to combine
independent "-m" options. Thus, one can use "-m 1 -m 6 -m
9".
-M low-high
Include library sequences (proteins only) with lengths
between low and high.
-n Force the query sequence to be treated as a DNA sequence.
This is particularly useful for query sequences that contain
a large number of ambiguous residues, e.g. transcription
factor binding sites.
-o Turn off default optimization of all scores greater than
OPTCUT. Sort results by "initn" scores (reduces the accuracy
of statistical estimates).
-p Force query to be treated as protein sequence.
-Q,-q
Quiet - does not prompt for any input. Writes scores and
alignments to the terminal or standard output file.
-r Specify match/mismatch scores for DNA comparisons. The
default is "+5/-4". "+3/-2" can perform better in some
cases.
-R file
Save a results summary line for every sequence in the
sequence library. The summary line includes the sequence
identifier, superfamily number (if available) position in
the library, and the similarity scores calculated. This
option can be used to evaluate the sensitivity and
selectivity of different search strategies (Pearson, 1995,
Pearson, 1998).
-s file
Specify the scoring matrix file. fasta3 uses the same
scoring matrices as Blast1.4/2.0. Several scoring matrix
files are included in the standard distribution. For
protein sequences: codaa.mat - based on minimum mutation
matrix; idnaa.mat - identity matrix; pam250.mat - the PAM250
matrix developed by Dayhoff et al. (Dayhoff et al., 1978);
pam120.mat - a PAM120 matrix. The default scoring matrix is
BLOSUM50 ("-s BL50"). Other matrices available from within
the program are: PAM250/"-s P250", PAM120/"-s P120",
PAM40/"-s P40", PAM20/"-s P20", MDM10 - MDM40/"-s M10 - M40"
(MDM are modern PAM matrices from Jones et al. (Jones et
al., 1992),), BLOSUM50, 62, and 80/"-s BL50", "-s BL62", "-s
BL80".
-S Treat lower-case characters in the query or library
sequences as "low-complexity" ("seg"-ed) residues.
Traditionally, the "seg" program (Wootton and
Federhen, 1993) is used to remove low complexity regions in
DNA sequences by replacing the residues with an "X". When
the "-S" option is used, the FASTA33 programs provide a
potentially more informative approach. With "-S", lower
case characters in the query or database sequences are
treated as "X"'s during the initial scan, but are treated as
normal residues during the final alignment display. Since
statistical significance is calculated from the similarity
score calculated during the library search, when the lower
case residues are "X"'s, low complexity regions will not
produce statistically significant matches. However, if a
significant alignment contains low complexity regions, their
alignmen is shown. With "-S", lower case characters may be
included in the alignment to indicate low complexity
regions, and the final alignment score may be higher than
the score obtained during the search.
The pseg program can be used to produce databases (or query
sequences) with lower case residues indicating low
complexity regions using the command:
pseg database.fasta -z 1 -q > database.lc_seg
(seg can also be used with some post processing, see
readme.v33tx.)
-U Treat the query sequence an RNA sequence. In addition to
selecting a DNA/RNA alphabet, this option causes changes to
the scoring matrix so that 'G:A' , 'T:C' or 'U:C' are scored
as 'G:G'.
-V str
It is now possible to specify some annotation characters
that can be included (and will be ignored), in the query
sequence file. Thus, One might have a file with:
"ACVS*ITRLFT?", where "*" and "?" are used to indicate
phosphorylation. By giving the option -V '*?', those
characters in the query will be moved to an "annotation
string", and alignments that include the annotated residues
will be highlighted with the appropriate character above the
sequence (on the number line).
-w # Line length (width) = number (<200)
-W # context length (default is 1/2 of line width -w) for
alignment, like fasta and ssearch, that provide additional
sequence context.
-x # Specify the penalty for a match to an 'X', independently of
the PAM matrix. Particularly useful for fastx3/fasty3,
where termination codons are encoded as 'X'.
-X Specifies offsets for the beginning of the query and library
sequence. For example, if you are comparing upstream
regions for two genes, and the first sequence contains 500
nt of upstream sequence while the second contains 300 nt of
upstream sequence, you might try:
fasta -X "-500 -300" seq1.nt seq2.nt
If the -X option is not used, FASTA assumes numbering starts
with 1. (You should double check to be certain the negative
numbering works properly.)
-y Set the width of the band used for calculating "optimized"
scores. For proteins and ktup=2, the width is 16. For
proteins with ktup=1, the width is 32 by default. For DNA
the width is 16.
-z -1,0,1,2,3,4,5
-z -1 turns off statistical calculations. z 0 estimates the
significance of the match from the mean and standard
deviation of the library scores, without correcting for
library sequence length. -z 1 (the default) uses a weighted
regression of average score vs library sequence length; -z 2
uses maximum likelihood estimates of Lambda and K; -z 3 uses
Altschul-Gish parameters (Altschul and Gish, 1996); -z 4 - 5
uses two variations on the -z 1 strategy. -z 1 and -z 2 are
the best methods, in general.
-z 11,12,14,15
estimate the statistical parameters from shuffled copies of
each library sequence. This doubles the time required for a
search, but allows accurate statistics to be estimated for
libraries comprised of a single protein family.
-Z db_size
set the apparent size of the database to be used when
calculating expectation E() values. If you searched a
database with 1,000 sequences, but would like to have the
E()-values calculated in the context of a 100,000 sequence
database, use '-Z 100000'.
-1 sort output by init1 score (for compatibility with FASTP -
do not use).
-3 translate only three forward frames
PepBank has been developed and is maintained by http://ric.csb.mgh.harvard.edu