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seqsort |
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)
% seqsort
Mandatory qualifiers (* if not always prompted): -mode menu Select mode * -psipath string Location of scop hits files (input) * -psiextn string Extension of scop hits files * -swisspath string Location of seqwords hits files * -swissextn string Extension of seqwords input files * -psifile string Name of file containing processed scop hits file (input) * -swissfile string Name of file containing processed seqwords hits file (input) -overlap integer number of overlapping residues required for merging of two hits [-hitsf] outfile Name of scop hits file (output) [-validf] outfile Name of validation file (output) 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 | |||||||
---|---|---|---|---|---|---|---|---|---|
-mode | Select mode |
|
1 | ||||||
-psipath | Location of scop hits files (input) | Any string is accepted | ./ | ||||||
-psiextn | Extension of scop hits files | Any string is accepted | .hits | ||||||
-swisspath | Location of seqwords hits files | Any string is accepted | ./ | ||||||
-swissextn | Extension of seqwords input files | Any string is accepted | .swissparse | ||||||
-psifile | Name of file containing processed scop hits file (input) | Any string is accepted | An empty string is accepted | ||||||
-swissfile | Name of file containing processed seqwords hits file (input) | Any string is accepted | An empty string is accepted | ||||||
-overlap | number of overlapping residues required for merging of two hits | Any integer value | 10 | ||||||
[-hitsf] (Parameter 1) |
Name of scop hits file (output) | Output file | seqsort.fam | ||||||
[-validf] (Parameter 2) |
Name of validation file (output) | Output file | seqsort.all | ||||||
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 |
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 |
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 |