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psiblasts |
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)
% psiblasts
Mandatory qualifiers: [-align] string Location of alignment files for input [-alignextn] string File extension of alignment files [-niter] integer Number of PSIBLAST iterations [-evalue] float Threshold E-value for inclusion in family [-maxhits] integer Maximum number of hits [-submatrix] string Residue substitution matrix [-families] outfile Name of families file for output [-logf] outfile Name of log file for the build 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 | |
---|---|---|---|
[-align] (Parameter 1) |
Location of alignment files for input | Any string is accepted | ./ |
[-alignextn] (Parameter 2) |
File extension of alignment files | Any string is accepted | .align |
[-niter] (Parameter 3) |
Number of PSIBLAST iterations | Any integer value | 1 |
[-evalue] (Parameter 4) |
Threshold E-value for inclusion in family | Any numeric value | 0.001 |
[-maxhits] (Parameter 5) |
Maximum number of hits | Any integer value | 1000 |
[-submatrix] (Parameter 6) |
Residue substitution matrix | Any string is accepted | ./EBLOSUM62 |
[-families] (Parameter 7) |
Name of families file for output | Output file | scop.hits |
[-logf] (Parameter 8) |
Name of log file for the build | Output file | psiblasts.log |
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 |
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 |