![]() |
seqsearch |
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)
% seqsearch
Mandatory qualifiers: [-escop] infile Name of scop classification file (embl format input) [-align] string Location of scop alignment files (input) [-alignextn] string Extension of scop 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 [-hits] string Location of scop hits files (output) [-hitsextn] string Extension of scop hits files -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 | |
---|---|---|---|
[-escop] (Parameter 1) |
Name of scop classification file (embl format input) | Input file | Escop.dat |
[-align] (Parameter 2) |
Location of scop alignment files (input) | Any string is accepted | ./ |
[-alignextn] (Parameter 3) |
Extension of scop alignment files | Any string is accepted | .salign |
-niter | Number of PSIBLAST iterations | Any integer value | 1 |
-evalue | Threshold E-value for inclusion in family | Any numeric value | 0.001 |
-maxhits | Maximum number of hits | Any integer value | 1000 |
-submatrix | Residue substitution matrix | Any string is accepted | ./EBLOSUM62 |
[-hits] (Parameter 4) |
Location of scop hits files (output) | Any string is accepted | ./ |
[-hitsextn] (Parameter 5) |
Extension of scop hits files | Any string is accepted | .hits |
-logf | Name of log file for the build | Output file | seqsearch.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 |
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 |
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 |