equicktandem

Function

Description

equicktandem scans a sequence for potential tandem repeats up to a specified size. The results can be used to run etandem on the candidate repeat lengths to identify genuine tandem repeats.

equicktandem is a simple program that looks for segments in which each base tends to match the base 'repeatsize' back, i.e. with an autocorrelation peak at 'repeatsize'. This can allow drift in the repeating sequence, i.e. it does not look for a consensus sequence for the whole repeat block (that is what etandem does). But it is much quicker than etandem. It does not account for gaps.

The score is +1 for a match to the corresponding base 'repeatsize' back and -1 for a mismatch.

Usage

Command line arguments


Input file format

The input for equicktandem is a nucleotide sequence USA.

Output file format

By default equicktandem writes a 'table' report file.

Data files

None.

Notes

None.

References

None.

Warnings

None.

Diagnostic Error Messages

None.

Exit status

It always exits with a status of 0.

Known bugs

None.

equicktandem identifies regions wich are likely to contain tanden repeats. tandem should then be run on those regions to confirm them and to get an accurate specification of the repeats. tandem runs slowly.

Author(s)

This program was originally written by

This application was modified for inclusion in EMBOSS by

History

Target users

Comments