profgen

 

Function

Generates various profiles for each alignment in a directory

Description

This is part of Jon Ison's protein structure analysis package.

This package is still being developed.

Please ignore this program until further details can be documented.

All further queries should go to Jon Ison. (Jon Ison)

Usage

Here is a sample session with profgen:

% profgen

Command line arguments

   Mandatory qualifiers (* if not always prompted):
   -infpath            string     Location of sequence alignment files (input)
   -infextn            string     Extension of sequence alignment files
   -type               menu       Select type
*  -threshold          integer    Enter threshold reporting percentage
*  -datafile           matrixf    Scoring matrix
*  -open               float      Gap opening penalty
*  -extension          float      Gap extension penalty
*  -smpfpath           string     Location of simple profile files (output)
*  -smpfextn           string     Extention of simple profile files
*  -gbpfpath           string     Location of Gribskov profile files (output)
*  -gbpfextn           string     Extension of Gribskov profile files
*  -hnpfpath           string     Location of Henikoff profile files (output)
*  -hnpfextn           string     Extention of Henikoff profile files

   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
-infpath Location of sequence alignment files (input) Any string is accepted ./
-infextn Extension of sequence alignment files Any string is accepted .ealign
-type Select type
F (Frequency)
G (Gribskov)
H (Henikoff)
F
-threshold Enter threshold reporting percentage Integer from 1 to 100 75
-datafile Scoring matrix Comparison matrix file in EMBOSS data path 'Epprofile' for Gribskov type, or EBLOSUM62
-open Gap opening penalty Any numeric value 3.0
-extension Gap extension penalty Any numeric value 0.3
-smpfpath Location of simple profile files (output) Any string is accepted ./tmp/
-smpfextn Extention of simple profile files Any string is accepted .freq
-gbpfpath Location of Gribskov profile files (output) Any string is accepted ./tmp/
-gbpfextn Extension of Gribskov profile files Any string is accepted .gribs
-hnpfpath Location of Henikoff profile files (output) Any string is accepted ./tmp/
-hnpfextn Extention of Henikoff profile files Any string is accepted .henik
Optional qualifiers Allowed values Default
(none)
Advanced qualifiers Allowed values Default
(none)

Input file format

Output file format

Data files

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
dichetParse dictionary of heterogen groups
hmmgenGenerates a hidden Markov model for each alignment in a directory
interfaceReads coordinate files and writes files of inter-chain residue-residue contact data
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 Jon Ison (jison@hgmp.mrc.ac.uk)

History

Written (date) - author.

Target users

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

Comments