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hmmgen |
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)
% hmmgen
Mandatory qualifiers: -infpath string Location of sequence alignment files (input) -infextn string Extention of sequence alignment files -outfpath string Location of HMM files (output) -outfextn string Extention of HMM 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 | Extention of sequence alignment files | Any string is accepted | .ealign |
-outfpath | Location of HMM files (output) | Any string is accepted | ./ |
-outfextn | Extention of HMM files | Any string is accepted | .hmm |
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 |
interface | Reads coordinate files and writes files of inter-chain residue-residue contact data |
profgen | Generates various profiles for each alignment in a directory |
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 |