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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 |
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 |