biosed

Function

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

Command line arguments


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 rarely used in proteins (e.g. U, J, O, etc), digits and punctuation characters.

Diagnostic Error Messages

None.

Exit status

Author(s)

History

Target users

Comments