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EMBOSS: biosed |
biosed was inspired by the useful UNIX utility sed which searches for a pattern in text and can replace or delete the found pattern.
If the target subsequence occurs more than once, then each instance of the target is replaced.
The target subsequence is not any sort of an ambiguity pattern, it is just a short sequence. A simple string match is done and if it exactly matches then the replacement is done. The matching is independent of the case of the sequence or the target - both uppercase and lowercase will match.
Replace all 'T's with 'U's to create a RNA sequence
% biosed em:hsfau hsfau.rna -target T -replace U
Replace all 'RGD' protein motifs with 'XXRGDXX'
% biosed sw:A4M1_HUMAN A4M1_HUMAN.pep -target RGD -replace XXRGDXX
Mandatory qualifiers (* if not always prompted): [-sequence] seqall Sequence database USA -target string Sequence section to match * -replace string Replacement sequence section [-outseq] seqout Output sequence USA Optional qualifiers: (none) Advanced qualifiers: -delete bool Delete the target sequence sections 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 | |
---|---|---|---|
[-sequence] (Parameter 1) |
Sequence database USA | Readable sequence(s) | Required |
-target | Sequence section to match | Any string is accepted | N |
-replace | Replacement sequence section | Any string is accepted | A |
[-outseq] (Parameter 2) |
Output sequence USA | Writeable sequence | <sequence>.format |
Optional qualifiers | Allowed values | Default | |
(none) | |||
Advanced qualifiers | Allowed values | Default | |
-delete | Delete the target sequence sections | Yes/No | No |
The sequence will be in uppercase.
Program name | Description |
---|---|
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 |
infoseq | Displays some simple information about sequences |
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 |
seqretall | Reads and writes (returns) a set of sequences one at a time |
seqretset | Reads and writes (returns) a set of sequences all at once |
seqretsplit | Reads and writes (returns) sequences in individual files |
splitter | Split a sequence into (overlapping) smaller sequences |
swissparse | Retrieves sequences from swissprot using keyword search |
trimest | Trim poly-A tails off EST sequences |
trimseq | Trim ambiguous bits off the ends of sequences |
vectorstrip | Strips out DNA between a pair of vector sequences |