EMBOSS: wordmatch

Program wordmatch

Function

Finds all exact matches of a given size between 2 sequences

Description

Finds all exact matches of a given minimum size between 2 sequences displaying the start points in each sequence and the match length.

Usage

Here is a sample session with wordmatch. 

% wordmatch sw:hba_human sw:hbb_human
Output file [hba_human.wordmatch]: 
Word size [4]: 

% more hba_human.wordmatch
FINALLY length = 3
 HBA_HUMAN  HBB_HUMAN Length
        58          63          5
        14          15          4
       116         121          4

Command line arguments 

   Mandatory qualifiers:
  [-asequence]         sequence   Sequence USA
  [-bsequence]         sequence   Sequence USA
  [-outfile]           outfile    Output file name
   -wordsize           integer    Word size

   Optional qualifiers: (none)
   Advanced qualifiers:
   -afeatout           featout    File for output of normal tab delimted gff's
   -bfeatout           featout    File for output of normal tab delimted gff's

Mandatory qualifiers Allowed values Default
[-asequence]
(Parameter 1)		 Sequence USA Readable sequence Required
[-bsequence]
(Parameter 2)		 Sequence USA Readable sequence Required
[-outfile]
(Parameter 3)		 Output file name Output file <sequence>.wordmatch
-wordsize Word size Integer 2 or more 4
Optional qualifiers Allowed values Default
(none)
Advanced qualifiers Allowed values Default
-afeatout File for output of normal tab delimted gff's Writeable feature table unknown.gff
-bfeatout File for output of normal tab delimted gff's Writeable feature table unknown.gff

Input file format

Any two sequence USAs of the same type (DNA or protein).

Output file format

Data files

Notes

References

Warnings

Diagnostic Error Messages

Exit status

0 if successfull.

Known bugs

See also
Program nameDescription
dotmatcherDisplays a thresholded dotplot of two sequences
polydotDisplays all-against-all dotplots of a set of sequences
seqmatchallDoes an all-against-all comparison of a set of sequences
stssearchSearches a DNA database for matches with a set of STS primers
supermatcherFinds a match of a large sequence against one or more sequences

Author(s)

This application was written by Ian Longden (il@sanger.ac.uk) Informatics Division, The Sanger Centre, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK.

History

Completed 27th November 1998.

Target users

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

Comments