| ## EMBOSS: biosed

# Program biosed

## Function

Replace or delete sequence sections

## Description

biosed is a simple sequence editing utility that searches for a target subsequence in one or more input sequences and replaces it with a specified second subsequence (or optionally just deletes the found target subsequence).

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.

## Usage

Here is a sample session with biosed:

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

## Command line arguments

       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

## Input file format

It reads the USA of one or more nucleic acid or protein sequences.

## Output file format

The edited sequence is output.

The sequence will be in uppercase.

## Data files

None.

## Notes

The edited sequence will be output in uppercase.

## References

None.

## Warnings

No check is made on the replacement subsequence.
Any text can be used as the replacement, including characters only used in proteins (e.g. D, E, F, etc.), characters not used in proteins (e.g. J, O, etc), digits and punctuation characters.

## Diagnostic Error Messages

None.

## Exit status

It always exits with status 0.

## Known bugs

None.

## See also

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
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
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
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

## Author(s)

This application was written by Alan Bleasby (ableasby@hgmp.mrc.ac.uk)

## History

Written (Jan 2002) - Alan Bleasby

## Target users

This program is intended to be used by everyone and everything, from naive users to embedded scripts.

## Comments