patmatdb

Function

Description

Takes a protein motif and compares it to a set of protein sequences.

It returns the number of matches there were between the motif and each matched sequence, length of match, start and end positions of match, and writes out an alignment.

Usage

Command line arguments


Input file format

patmatdb reads in one or more protein sequence USAs.

Pattern specification

Patterns for patmatdb are based on the format of pattern used in the PROSITE database, with the difference that the terminating dot '.' and the hyphens, '-', between the characters are optional.

The PROSITE pattern definition from the PROSITE documentation follows.

For example, in SWISSPROT entry 100K_RAT you can look for the pattern:

[DE](2)HS{P}X(2)PX(2,4)C

This means: Two Asps or Glus in any order followed by His, Ser, any residue other then Pro, then two of any residue followed by Pro followed by two to four of any residue followed by Cys.

The search is case-independent, so 'AAA' matches 'aaa'.

Output file format

By default patmatdb writes a 'dbmotif' report file.

Data files

None.

Notes

None.

References

  1. Bairoch, A., Bucher P. (1994) PROSITE: recent developments. Nucleic Acids Research, Vol 22, No.17 3583-3589.
  2. Bairoch, A., (1992) PROSITE: a dictionary of sites and patterns in proteins. Nucleic Acids Research, Vol 20, Supplement, 2013-2018.
  3. Peek, J., O'Reilly, T., Loukides, M., (1997) Unix Power Tools, 2nd Edition.
  4. Gusfield, D., (1997) Algorithms on strings, Trees and Sequences.
  5. Sedgewick, R,. (1990) Algorithms in C.

Warnings

None.

Diagnostic Error Messages

None.

Exit status

It always exits with status 0

Known bugs

None.

Author(s)

History

Target users

Comments