jaspscan

Function

Description

jaspscan scans one or more DNA sequences for transcription factor binding sites from the JASPAR database. Matches are searched for using fast sequence word-matching, optionally allowing mismatches. Because the binding sites are so small, there will be many spurious (false positive) matches.

An output file is written with information on the matches, including sequence ID and accession number, the start and end positions of the match in an input sequence and the sequence of the region where a match has been found. Binding factor information, where available, is given at the end of the matches for each matching entry.

Usage

Command line arguments

Input file format

jaspscan reads any normal sequence USAs.

Output file format

jaspscan outputs a report format file.

Data files

Notes

None.

References

  1. DNA binding sites: representation and discovery Bioinformatics. 2000 Jan;16(1):16-23
  2. Applied bioinformatics for the identification of regulatory elements Nat Rev Genet. 2004 Apr;5(4):276-87

Warnings

None.

Diagnostic Error Messages

None.

Exit status

It always exits with status 0.

Known bugs

None.

Author(s)

History

Target users

Comments