EMBOSS: seqmatchall

Program seqmatchall

Function

Does an all-against-all comparison of a set of sequences

Description

This takes a set of sequences and does an all-against-all pairwise comparison of words (fragments of the sequences of a specified fixed size) in the sequences, finding regions of identity between any two sequences.

The larger the specified word size, the faster the comparison will proceed. Regions whose stretches of identity are shorter than the word size will be missed. You should therefore choose a word size that is small enough to find those regions of similarity you are interested in within a reasonable time-frame.

Usage

Here is a sample session with seqmatchall. We use an increased word size to avoid accidental matches.


% seqmatchall
Does an all-against-all comparison of a set of sequences
Input sequence set: embl:eclac*
Word size [4]: 15
Output file [outfile.seqmatchall]:

Command line arguments

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

   Optional qualifiers: (none)
   Advanced qualifiers: (none)
   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 set USA Readable sequences Required

-wordsize Word size Integer 2 or more 4

[-outfile]
(Parameter 2) Output file name Output file <sequence>.seqmatchall

Optional qualifiers Allowed values Default

(none)

Advanced qualifiers Allowed values Default

(none)

Mandatory qualifiers	Allowed values	Default
[-sequence] (Parameter 1)	Sequence set USA	Readable sequences	Required
-wordsize	Word size	Integer 2 or more	4
[-outfile] (Parameter 2)	Output file name	Output file	<sequence>.seqmatchall
Optional qualifiers	Allowed values	Default
(none)
Advanced qualifiers	Allowed values	Default
(none)

Input file format

A set of sequences. This can be a list file of sequence or a wildcarded set of sequences from a database or all sequences from a database, or a wildcarded set of sequence files.

The sequences must be all either protein or nucleic.

Output file format

Here is the output from the example run.

ECLAC (the complete E.coli lac operon) matches ECLACI ECLACZ ECLACY and ECLACA (the individual genes), and there is a short overlap between ECLACY and the flanking genes ECLACZ and ECLACA


1832  5645 7477 ECLAC 0 1832 ECLACA
1113  48 1161 ECLAC 0 1113 ECLACI
1500  4304 5804 ECLAC 0 1500 ECLACY
3078  1286 4364 ECLAC 0 3078 ECLACZ
158  1 159 ECLACA 1342 1500 ECLACY
59  1 60 ECLACY 3019 3078 ECLACZ

The output is a list of regions of identity in pairs of sequences, each consisting of one line with 7 columns of data separated by TABs or space characters. The columns of data consist of:

The length of the region of identity.
The start position in sequence 1.
The end position in sequence 1.
The name of sequence 1.
The start position in sequence 2.
The end position in sequence 2.
The name of sequence 2.

Data files

Notes

The larger the word size, the faster the comparisons will proceed, but regions of identitly smaller than the word size will not be reported.

References

Warnings

Diagnostic Error Messages

Exit status

It exits with a status of 0.

Known bugs

Program name	Description
matcher	Finds the best local alignments between two sequences
supermatcher	Finds a match of a large sequence against one or more sequences
water	Smith-Waterman local alignment
wordmatch	Finds all exact matches of a given size between 2 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

Target users

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