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

Here is an example using an increased word size to avoid accidental matches: 


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

Go to the input files for this example
Go to the output files for this example

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                boolean    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)

Input file format

seqmatchall reads a set of sequence USAs.

The sequences must be either all protein or all nucleic acid.

Input files for usage example

'tembl:eclac*' is a sequence entry in the example nucleic acid database 'tembl'

Output file format

Output files for usage example

File: eclac.seqmatchall

1832  5646 7477 ECLAC 1 1832 ECLACA
1113  49 1161 ECLAC 1 1113 ECLACI
1500  4305 5804 ECLAC 1 1500 ECLACY
3078  1287 4364 ECLAC 1 3078 ECLACZ
159  1 159 ECLACA 1342 1500 ECLACY
60  1 60 ECLACY 3019 3078 ECLACZ

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

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:

Data files

None.

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

None.

Warnings

None.

Diagnostic Error Messages

None.

Exit status

It exits with a status of 0.

Known bugs

None.

See also

Program nameDescription
matcherFinds the best local alignments between two sequences
supermatcherFinds a match of a large sequence against one or more sequences
waterSmith-Waterman local alignment
wordmatchFinds all exact matches of a given size between 2 sequences

polydot will give a graphical view of the same matches.

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

1999 - written.

Target users

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

Comments