swissparse

 

Function

Retrieves sequences from swissprot using keyword search

Description

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Usage

Here is a sample session with swissparse:

% swissparse

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Command line arguments

   Mandatory qualifiers:
  [-keyfile]           infile     Name of keywords file for input
  [-spfile]            infile     Name of swissprot database to read
  [-outfile]           outfile    Name of search results file for output

   Optional qualifiers: (none)
   Advanced qualifiers: (none)
   General qualifiers:
  -help                boolean    Report command line options. More
                                  information on associated and general
                                  qualifiers can be found with -help -verbose


Mandatory qualifiers Allowed values Default
[-keyfile]
(Parameter 1)
Name of keywords file for input Input file scop.terms
[-spfile]
(Parameter 2)
Name of swissprot database to read Input file ./seq.dat
[-outfile]
(Parameter 3)
Name of search results file for output Output file scop.seqs
Optional qualifiers Allowed values Default
(none)
Advanced qualifiers Allowed values Default
(none)

Input file format

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Output file format

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Data files

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Notes

None.

References

None.

Warnings

None.

Diagnostic Error Messages

None.

Exit status

It always exits with status 0.

Known bugs

None.

See also

Program nameDescription
biosedReplace or delete sequence sections
coderetExtract CDS, mRNA and translations from feature tables
cutseqRemoves a specified section from a sequence
degapseqRemoves gap characters from sequences
descseqAlter the name or description of a sequence
entretReads and writes (returns) flatfile entries
extractfeatExtract features from a sequence
extractseqExtract regions from a sequence
listorWrites a list file of the logical OR of two sets of sequences
maskfeatMask off features of a sequence
maskseqMask off regions of a sequence
newseqType in a short new sequence
noreturnRemoves carriage return from ASCII files
notseqExcludes a set of sequences and writes out the remaining ones
nthseqWrites one sequence from a multiple set of sequences
pasteseqInsert one sequence into another
revseqReverse and complement a sequence
seqretReads and writes (returns) sequences
seqretsplitReads and writes (returns) sequences in individual files
showfeatShow features of a sequence
skipseqReads and writes (returns) sequences, skipping the first few
splitterSplit a sequence into (overlapping) smaller sequences
trimestTrim poly-A tails off EST sequences
trimseqTrim ambiguous bits off the ends of sequences
unionReads sequence fragments and builds one sequence
vectorstripStrips out DNA between a pair of vector sequences
yankReads a sequence range, appends the full USA to a list file

Author(s)

This application was written by Alan Bleasby (ableasby@hgmp.mrc.ac.uk) **************** EDIT HERE ****************

History

Written (date) - author. **************** EDIT HERE ****************

Target users

This program is intended to be used by everyone and everything, from naive users to embedded scripts.

Comments