
                             EMBOSS: swissparse
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                              Program 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                bool       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 name                          Description
   biosed       Replace or delete sequence sections
   coderet      Extract CDS, mRNA and translations from feature tables
   cutseq       Removes a specified section from a sequence
   degapseq     Removes gap characters from sequences
   descseq      Alter the name or description of a sequence
   entret       Reads and writes (returns) flatfile entries
   extractfeat  Extract features from a sequence
   extractseq   Extract regions from a sequence
   listor       Writes a list file of the logical OR of two sets of sequences
   maskfeat     Mask off features of a sequence
   maskseq      Mask off regions of a sequence
   newseq       Type in a short new sequence
   noreturn     Removes carriage return from ASCII files
   notseq       Excludes a set of sequences and writes out the remaining ones
   nthseq       Writes one sequence from a multiple set of sequences
   pasteseq     Insert one sequence into another
   revseq       Reverse and complement a sequence
   seqret       Reads and writes (returns) sequences
   seqretsplit  Reads and writes (returns) sequences in individual files
   showfeat     Show features of a sequence
   splitter     Split a sequence into (overlapping) smaller sequences
   trimest      Trim poly-A tails off EST sequences
   trimseq      Trim ambiguous bits off the ends of sequences
   union        Reads sequence fragments and builds one sequence
   vectorstrip  Strips out DNA between a pair of vector sequences
   yank         Reads 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)
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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
