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profgen |
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)
% profgen
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 | ||||||
-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) |
Program name | Description |
---|---|
contacts | Reads coordinate files and writes files of intra-chain residue-residue contact data |
dichet | Parse dictionary of heterogen groups |
hmmgen | Generates a hidden Markov model for each alignment in a directory |
interface | Reads coordinate files and writes files of inter-chain residue-residue contact data |
psiblasts | Runs PSI-BLAST given scopalign alignments |
scopalign | Generate alignments for families in a scop classification file by using STAMP |
scoprep | Reorder scop classificaiton file so that the representative structure of each family is given first |
scopreso | Removes low resolution domains from a scop classification file |
seqalign | Generate extended alignments for families in a scop families file by using CLUSTALW with seed alignments |
seqsearch | Generate files of hits for families in a scop classification file by using PSI-BLAST with seed alignments |
seqsort | Reads multiple files of hits and writes a non-ambiguous file of hits (scop families file) plus a validation file |
seqwords | Generate file of hits for scop families by searching swissprot with keywords |
siggen | Generates a sparse protein signature from an alignment and residue contact data |
sigscan | Scans a signature against swissprot and writes a signature hits files |