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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
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| 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 |