![]() |
EMBOSS: 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 [-overlap] integer number of overlapping residues required for merging of two hits * -psipath string Location of psiblasts hits files * -psiextn string Extension of psiblasts hits files * -swisspath string Location of swissparse hits files * -swissextn string Extension of swissparse input files * -psifile string Name of file containing sorted psiblasts results * -swissfile string Name of file containing sorted swissparse results [-outfile] string Name of output file Optional qualifiers: (none) Advanced qualifiers: (none) General qualifiers: -help bool report command line options. More information on associated and general qualifiers can be found with -help -verbose |
Mandatory qualifiers | Allowed values | Default | |||||||
---|---|---|---|---|---|---|---|---|---|
[-mode] (Parameter 1) |
Select mode |
|
1 | ||||||
[-overlap] (Parameter 2) |
number of overlapping residues required for merging of two hits | Any integer value | 10 | ||||||
-psipath | Location of psiblasts hits files | Any string is accepted | ./ | ||||||
-psiextn | Extension of psiblasts hits files | Any string is accepted | .psiblasts | ||||||
-swisspath | Location of swissparse hits files | Any string is accepted | ./ | ||||||
-swissextn | Extension of swissparse input files | Any string is accepted | .swissparse | ||||||
-psifile | Name of file containing sorted psiblasts results | Any string is accepted | An empty string is accepted | ||||||
-swissfile | Name of file containing sorted swissparse results | Any string is accepted | An empty string is accepted | ||||||
[-outfile] (Parameter 3) |
Name of output file | Any string is accepted | An empty string is accepted | ||||||
Optional qualifiers | Allowed values | Default | |||||||
(none) | |||||||||
Advanced qualifiers | Allowed values | Default | |||||||
(none) |
Program name | Description |
---|---|
contacts | Reads coordinate files and writes contact files |
dichet | Parse dictionary of heterogen groups |
interface | Reads coordinate files and writes inter-chain contact files |
psiblasts | Runs PSI-BLAST given scopalign alignments |
scopalign | Generate alignments for SCOP families |
siggen | Generates a sparse protein signature |
sigscan | Scans a sparse protein signature against swissprot |