
                               EMBOSS: biosed
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                                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
