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Home | NucleicAcid | Protein | Database | PCR | Alignment | Tools | Bookmarklets | Customize

Copyright © 2000 Malay Kumar Basu
Send your comments/suggestions/bug-report to me:
curiouser@ccmb.ap.nic.in
Disclaimer
entrez protein search
Search exclude patents   
From To
Use the format YYYY/MM/DD; month and day are optional.
protparam
Enter a SWISS-PROT/TrEMBL accession number or a sequence identifier
psipred
E-Mail address
Short name of sequence
Prediction Method
Predict Secondary Structure (PSIpred)
Predict Transmembrane Topology (MEMSAT)
Fold Recognition (GenTHREADER)
Fold Recognition (GenTHREADER with multiple sequences)
scanprosite
SWISS-PROT/TrEMBL accession number or a sequence identifier
Exclude patterns with a high probability of occurrence
Entrez
Search for a protein sequence using Enterz at NCBI server. Input type-key-words. Required option-none.
ProtParam
Calculate different physico-chemical parameters of a protein sequence. Input type-protein sequence. Required option-none.
PSIPred
Secondary structure Prediction. Winner of Critical Assessment of Protein Structure Prediction 1998 (CASP3). Correct upto 77%. Input type-protein sequence. Required option- email address.
ScanProsite
Search for PROSITE pattern in your protein sequence. Input type-protein sequence. Required option-none.
ANTIGENIC
Finds antigenic sites in proteins (EMBOSS). Input type: sequence -- PureProtein [sequences] (-sequence).
Required options: email sequence minlen outfile.

antigenic

Your email:

Minimum length (-minlen)

outfile (-outfile)

BACKTRANSEQ
Back translate a protein sequence (EMBOSS). Input type: sequence -- PureProtein [single sequence] (-sequence).
Required options: email sequence outfile.

backtranseq

Your email:

cfile [codon usage table name] (-cfile)

outfile (-outfile)

Output format for: outfile

CHARGE
Protein charge plot (EMBOSS). Input type: seqall -- protein [sequences] (-seqall).
Required options: email seqall.

charge

Your email:

Window (-window)

Amino acid property data file name (-aadata)

Produce graphic (-plot)

graph (-graph)

outfile (-outfile)

CHECKTRANS
Reports STOP codons and ORF statistics of a protein sequence (EMBOSS). Input type: sequence -- stopprotein [sequences] (-sequence).
Required options: email sequence orfml report featout.

checktrans

Your email:

Minimum ORF Length to report (-orfml)

report (-report)

Sequence file to hold output ORF sequences (-outseq)

Output format for: Sequence file to hold output ORF sequences

feature file for output (-featout)

COMPSEQ
Counts the composition of dimer/trimer/etc words in a sequence (EMBOSS). Input type: sequence [sequences] (-sequence).
Required options: email sequence word outfile.

compseq

Your email:

Word size to consider (e.g. 2=dimer) (-word)


'compseq' file to use for expected word frequencies (-infile)

Frame of word to look at (0=all frames) (-frame)

Ignore the amino acids B and Z and just count them as 'Other' (-ignorebz)

Count words in the forward and reverse sense (-reverse)

outfile (-outfile)

Display the words that have a frequency of zero (-zerocount)

DIGEST
Protein proteolytic enzyme or reagent cleavage digest (EMBOSS). Input type: sequencea -- Protein [single sequence] (-sequencea).
Required options: email sequencea menu outfile.

digest

Your email:

Select number -- Enzymes and Reagents (-menu)

Allow unfavoured cuts (-unfavoured)

Amino acid data file (-aadata)

Show overlapping partials (-overlap)

Show all partials (-allpartials)

outfile (-outfile)

EMOWSE
Protein identification by mass spectrometry (EMBOSS). Input type: sequences -- protein [sequences] (-sequences).
Required options: email sequences infile weight enzyme.

emowse

Your email:


Name of molecular weight data file (-infile)

Whole sequence molwt (-weight)

Enzyme or reagent -- Enzymes and reagents (-enzyme)

Amino acid data file (-aadata)

Allowed whole sequence weight variability (-pcrange)

Frequencies file (-frequencies)

tolerance -- enter a number (-tolerance)

Partials factor (-partials)

outfile (-outfile)

FREAK
Residue/base frequency table or plot (EMBOSS). Input type: seqall -- any [sequences] (-seqall).
Required options: email seqall letters.

freak

Your email:

Residue letters (-letters)

Stepping value (-step)

Averaging window (-window)

Produce graphic (-plot)

graph (-graph)

outfile (-outfile)

FUZZPRO
Protein pattern search (EMBOSS). Input type: sequence -- protein [sequences] (-sequence).
Required options: email sequence pattern mismatch outf.

fuzzpro

Your email:

Search pattern (-pattern)

Number of mismatches (-mismatch)

Show mismatches (-mmshow)

Show accession numbers (-accshow)

Show USA (-usashow)

Show descriptions (-descshow)

outf (-outf)

FUZZTRAN
Protein pattern search after translation (EMBOSS). Input type: sequence -- dna [sequences] (-sequence).
Required options: email sequence pattern mismatch frame table outf.

fuzztran

Your email:

Search pattern (-pattern)

Number of mismatches (-mismatch)

Frame(s) to translate -- Translation frames (-frame)

Code to use -- Genetic codes (-table)

outf (-outf)

Show mismatches (-mmshow)

Show accession numbers (-accshow)

Show USA (-usashow)

Show descriptions (-descshow)

HELIXTURNHELIX
Report nucleic acid binding motifs (EMBOSS). Input type: sequence -- PureProtein [sequences] (-sequence).
Required options: email sequence outfile.

helixturnhelix

Your email:

Mean value (-mean)

Standard Deviation value (-sd)

Minimum SD (-minsd)

Use the old (1987) weight data (-eightyseven)

outfile (-outfile)

HMOMENT
Hydrophobic moment calculation (EMBOSS). Input type: seqall -- pureprotein [sequences] (-seqall).
Required options: email seqall.

hmoment

Your email:

Window (-window)

Alpha helix angle (degrees) (-aangle)

Beta sheet angle (degrees) (-bangle)

Graph marker line (-baseline)

Produce graphic (-plot)

Plot two graphs (-double)

graph (-graph)

outfile (-outfile)

IEP
Calculates the isoelectric point of a protein (EMBOSS). Input type: sequencea -- pureprotein [sequences] (-sequencea).
Required options: email sequencea.

iep

Your email:

pH step value (-step)

Number of N-termini (-amino)

Include charge at N and C terminus (-termini)

Plot charge vs pH (-plot)

Write results to a file (-report)

graph (-graph)

outfile (-outfile)

INTERFACE
Reads coordinate files and writes inter-chain contact files (EMBOSS). Input type: .
Required options: email in out thresh.

interface

Your email:


Coordinate file for input (embl-like format) (-in)

Contact file for output (-out)

Threshold contact distance (-thresh)

Threshold ignore distance (-ignore)

Name of data file with van der Waals radii (-vdwf)

Name of log file for the build (-conerrf)

MSBAR
Mutate sequence beyond all recognition (EMBOSS). Input type: sequence -- any [sequences] (-sequence).
Required options: email sequence count point block codon outseq.

msbar

Your email:

Number of times to perform the mutation operations (-count)

Do 'codon' and 'block' operations in frame (-inframe)

Minimum size for a block mutation (-minimum)

Maximum size for a block mutation (-maximum)

outseq (-outseq)

Output format for: outseq

MWFILTER
Filter noisy molwts from mass spec output (EMBOSS). Input type: .
Required options: email infile tolerance outfile.

mwfilter

Your email:


Molecular weight file input (-infile)

ppm tolerance (-tolerance)

Data file of noisy molecular weights (-datafile)

outfile (-outfile)

OCTANOL
Displays protein hydropathy (EMBOSS). Input type: sequencea -- pureprotein [single sequence] (-sequencea).
Required options: email sequencea graph.

octanol

Your email:


White-Wimley data file (Ewhite-wimley.dat) (-datafile)

window size (-width)

graph (-graph)

Display the octanol plot (-octanolplot)

Display the interface plot (-interfaceplot)

Do not display the difference plot (-differenceplot)

ODDCOMP
Finds protein sequence regions with a biased composition (EMBOSS). Input type: sequence -- Protein [sequences] (-sequence).
Required options: email sequence compdata window outfile.

oddcomp

Your email:


'compseq' file to use for expected word frequencies (-compdata)

Window size to consider (e.g. 30 aa) (-window)

Ignore the amino acids B and Z and just count them as 'Other' (-ignorebz)

outfile (-outfile)

PATMATDB
Search a protein sequence with a motif (EMBOSS). Input type: sequence -- Protein [sequences] (-sequence).
Required options: email sequence motif outfile.

patmatdb

Your email:

Protein motif to search for (-motif)

outfile (-outfile)

PATMATMOTIFS
Search a PROSITE motif database with a protein sequence (EMBOSS). Input type: sequence -- Protein [single sequence] (-sequence).
Required options: email sequence outfile.

patmatmotifs

Your email:

Provide full documentation for matching patterns (-full)

Ignore simple patterns (-prune)

outfile (-outfile)

PEPCOIL
Predicts coiled coil regions (EMBOSS). Input type: sequence -- PureProtein [sequences] (-sequence).
Required options: email sequence window outfile.

pepcoil

Your email:

Window size (-window)

Report coiled coil regions (-coil)

Show coil frameshifts (-frame)

Report non coiled coil regions (-other)

outfile (-outfile)

PEPINFO
Plots simple amino acid properties in parallel (EMBOSS). Input type: inseq -- protein [single sequence] (-inseq).
Required options: email inseq outfile.

pepinfo

Your email:

graph (-graph)

outfile (-outfile)

plot histogram of general properties (-generalplot)

plot graphs of hydropathy (-hydropathyplot)

Window size for hydropathy averaging (-hwindow)

Enter user defined file of amino acid properties or leave blank (-aaproperties)

Enter user defined file of hydropathy data or leave blank (-aahydropathy)

PEPNET
Displays proteins as a helical net (EMBOSS). Input type: sequence -- Protein [single sequence] (-sequence).
Required options: email sequence.

pepnet

Your email:

Prompt for amphipathic residue marking (-amphipathic)

Mark as squares (-squares)

Mark as diamonds (-diamonds)

Mark as octagons (-octags)

Display as data (-data)

graph [device to be displayed on] (-graph)

PEPSTATS
Protein statistics (EMBOSS). Input type: sequencea -- PureProtein [single sequence] (-sequencea).
Required options: email sequencea.

pepstats

Your email:

Include charge at N and C terminus (-termini)

Amino acid data file (-aadata)

outfile (-outfile)

PEPWHEEL
Shows protein sequences as helices (EMBOSS). Input type: sequence -- Protein [single sequence] (-sequence).
Required options: email sequence.

pepwheel

Your email:

Plot the wheel (-wheel)

Number of steps (-steps)

Number of turns (-turns)

Prompt for amphipathic residue marking (-amphipathic)

Mark as squares (-squares)

Mark as diamonds (-diamonds)

Mark as octagons (-octags)

Display as data (-data)

outfile (-outfile)

graph [device to be displayed on] (-graph)

PEPWINDOW
Displays protein hydropathy (EMBOSS). Input type: sequencea -- pureprotein [single sequence] (-sequencea).
Required options: email sequencea.

pepwindow

Your email:


nakai database file (-datafile)

window size (-length)

graph (-graph)

PEPWINDOWALL
Displays protein hydropathy of a set of sequences (EMBOSS). Input type: Sequences file to be read in (-msf).
Required options: email msf graph.

pepwindowall

Your email:


nakai database file (-datafile)

window size (-length)

graph (-graph)

PREG
Regular expression search of a protein sequence (EMBOSS). Input type: sequence -- protein [sequences] (-sequence).
Required options: email sequence pattern outfile.

preg

Your email:

Regular expression pattern (-pattern)

outfile (-outfile)

PROFIT
Scan a sequence or database with a matrix or profile (EMBOSS). Input type: sequence -- any [sequences] (-sequence).
Required options: email infile sequence outfile.

profit

Your email:


Profile or matrix file (-infile)

outfile (-outfile)

PROPHECY
Creates matrices/profiles from multiple alignments (EMBOSS). Input type: sequence -- gapany [set of sequences] (-sequence).
Required options: email sequence type name outf.

prophecy

Your email:

Select type -- Profile type (-type)

Enter a name for the profile (-name)

Enter threshold reporting percentage (-threshold)

Scoring matrix (-datafile)

Gap opening penalty (-open)

Gap extension penalty (-extension)

outf (-outf)

PROPHET
Gapped alignment for profiles (EMBOSS). Input type: sequence -- any [sequences] (-sequence).
Required options: email sequence infile gapopen gapextend outfile.

prophet

Your email:


Profile or matrix file (-infile)

Gap opening coefficient (-gapopen)

Gap extension coefficient (-gapextend)

outfile (-outfile)

PSCAN
Scans proteins using PRINTS (EMBOSS). Input type: sequence -- Protein [sequences] (-sequence).
Required options: email sequence emin emax outfile.

pscan

Your email:

Minimum number of elements per fingerprint (-emin)

Maximum number of elements per fingerprint (-emax)

outfile (-outfile)

SHUFFLESEQ
Shuffles a set of sequences maintaining composition (EMBOSS). Input type: sequence -- any [sequences] (-sequence).
Required options: email sequence outseq.

shuffleseq

Your email:

Number of shuffles (-shuffle)

outseq (-outseq)

Output format for: outseq

SIGCLEAVE
Reports protein signal cleavage sites (EMBOSS). Input type: sequence -- PureProtein [sequences] (-sequence).
Required options: email sequence minweight outfile.

sigcleave

Your email:

Minimum weight (-minweight)

Use prokaryotic cleavage data (-prokaryote)

Pval (-pval)

Nval (-nval)

outfile (-outfile)

SIGGEN
Generates a sparse protein signature (EMBOSS). Input type: .
Required options: email algpath algextn sparsity seqoption conoption sigpath sigextn.

siggen

Your email:


Location of alignment files for input (-algpath)

Extension of alignment files for input (-algextn)

% sparsity of signature (-sparsity)

Generate a randomised signature (-randomise)

Substitution matrix to be used (-datafile)

Ignore alignment positions making less than a threshold number of contacts (-filtercon)

Threshold contact number (-conthresh)

Location of contact files for input (-conpath)

Extension of contact files (-conextn)

Location of coordinate files for input (embl-like format) (-cpdbpath)

Extension of coordinate files (embl-like format) (-cpdbextn)

Ignore alignment postitions with post_similar value of 0 (-filterpsim)

Extension of signature files for output (-sigextn)

SIGSCAN
Scans a sparse protein signature against swissprot (EMBOSS). Input type: Name of sequence database to search (-database).
Required options: email sigin database targetf thresh sub gapo gape nterm nhits hitsf alignf.

sigscan

Your email:


Name of signature file for input (-sigin)


Name of (optionally grouped) scop families file for input (-targetf)

Minimum length (residues) of overlap required for two hits with the same code to be counted as the same hit. (-thresh)

Residue substitution matrix (-sub)

Gap insertion penalty (-gapo)

Gap extension penalty (-gape)

Select number -- N-terminal matching options (-nterm)

Number of hits to output (-nhits)

Name of signature hits file for output (-hitsf)

Name of signature alignments file for output (-alignf)

TMAP
Displays membrane spanning regions (EMBOSS). Input type: Sequences file to be read in (-msf).
Required options: email msf.

tmap

Your email:

graph (-graph)

outfile (-outfile)

PESTFIND
Find PEST (proline, glutamic acid, serine and threonin) sequences from a single protein sequence. Input type: Sequence file.
Required options: email in_file minimum_aa.

pestfind

Your email:

Minimum AA number between positive flanks

Print invalid sequences

PLSEARCH
search protein sequences for similarity to AACC patterns. Input type: Protein sequence File.
Required options: email protein outfile.

plsearch

Your email:

Results file

Maximum number of alignments

prose
Prosite Pattern search. Input type: Protein Sequence File.
Required options: email infile.

prose

Your email:


Pattern List File (-l)

report occurences (-m)

search case-sensitive

warn of inproper prosite pattern syntaxe

include abundant patterns

SAPS
Statistical Analysis of Protein Sequences. Input type: Protein sequence(s) File.
Required options: email seq.

saps

Your email:

Generate documented output (-d)

Generate terse output (-t)

Generate verbose output (-v)

Append computer-readable table summary output (-T)

Use this specie for quantile comparisons (-s)

Count H as positive charge (-H)

Analyze spacings of amino acids X, Y, .... (-a)

PSORT
predicts protein subcellular localization sites from their amino acid sequences (Psort version II). Input type: Protein sequence file.
Required options: email psort2 seqfile.

psort2

Your email:

Verbose mode