dichet

 

Function

Parse dictionary of heterogen groups

Description

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Usage

Here is a sample session with dichet:

% dichet

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Command line arguments

   Mandatory qualifiers (* if not always prompted):
  [-inf]               infile     Name of raw input file (dictionary of
                                  heterogen groups)
  [-dogrep]            boolean    Search a directory of files with keywords?
  [-outf]              outfile    Name of output file
*  -path               string     Directory to search with keywords
*  -extn               string     Exension of files to search in above
                                  directory

   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
[-inf]
(Parameter 1)
Name of raw input file (dictionary of heterogen groups) Input file Required
[-dogrep]
(Parameter 2)
Search a directory of files with keywords? Yes/No No
[-outf]
(Parameter 3)
Name of output file Output file <sequence>.dichet
-path Directory to search with keywords Any string is accepted ./
-extn Exension of files to search in above directory Any string is accepted .ent
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
contactsReads coordinate files and writes files of intra-chain residue-residue contact data
hmmgenGenerates a hidden Markov model for each alignment in a directory
interfaceReads coordinate files and writes files of inter-chain residue-residue contact data
profgenGenerates various profiles for each alignment in a directory
psiblastsRuns PSI-BLAST given scopalign alignments
scopalignGenerate alignments for families in a scop classification file by using STAMP
scoprepReorder scop classificaiton file so that the representative structure of each family is given first
scopresoRemoves low resolution domains from a scop classification file
seqalignGenerate extended alignments for families in a scop families file by using CLUSTALW with seed alignments
seqsearchGenerate files of hits for families in a scop classification file by using PSI-BLAST with seed alignments
seqsortReads multiple files of hits and writes a non-ambiguous file of hits (scop families file) plus a validation file
seqwordsGenerate file of hits for scop families by searching swissprot with keywords
siggenGenerates a sparse protein signature from an alignment and residue contact data
sigscanScans a signature against swissprot and writes a signature hits files

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