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EMBOSS: swissparse |
% swissparse**************** EDIT HERE ****************
Mandatory qualifiers:
[-keyfile] infile Name of keywords file for input
[-spfile] infile Name of swissprot database to read
[-outfile] outfile Name of search results file for output
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
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| Mandatory qualifiers | Allowed values | Default | |
|---|---|---|---|
| [-keyfile] (Parameter 1) |
Name of keywords file for input | Input file | scop.terms |
| [-spfile] (Parameter 2) |
Name of swissprot database to read | Input file | ./seq.dat |
| [-outfile] (Parameter 3) |
Name of search results file for output | Output file | scop.seqs |
| Optional qualifiers | Allowed values | Default | |
| (none) | |||
| Advanced qualifiers | Allowed values | Default | |
| (none) | |||
| Program name | Description |
|---|---|
| biosed | Replace or delete sequence sections |
| coderet | Extract CDS, mRNA and translations from feature tables |
| cutseq | Removes a specified section from a sequence |
| degapseq | Removes gap characters from sequences |
| descseq | Alter the name or description of a sequence |
| entret | Reads and writes (returns) flatfile entries |
| extractfeat | Extract features from a sequence |
| extractseq | Extract regions from a sequence |
| listor | Writes a list file of the logical OR of two sets of sequences |
| maskfeat | Mask off features of a sequence |
| maskseq | Mask off regions of a sequence |
| newseq | Type in a short new sequence |
| noreturn | Removes carriage return from ASCII files |
| notseq | Excludes a set of sequences and writes out the remaining ones |
| nthseq | Writes one sequence from a multiple set of sequences |
| pasteseq | Insert one sequence into another |
| revseq | Reverse and complement a sequence |
| seqret | Reads and writes (returns) sequences |
| seqretsplit | Reads and writes (returns) sequences in individual files |
| showfeat | Show features of a sequence |
| splitter | Split a sequence into (overlapping) smaller sequences |
| trimest | Trim poly-A tails off EST sequences |
| trimseq | Trim ambiguous bits off the ends of sequences |
| union | Reads sequence fragments and builds one sequence |
| vectorstrip | Strips out DNA between a pair of vector sequences |
| yank | Reads a sequence range, appends the full USA to a list file |