Function

Description

patmatdb searches the input protein sequences for the specified sequence motif. The output is a standard EMBOSS report file including the number of matches between the motif and each input sequence, length of match, start and end positions of match, and the motif-sequence alignment. 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.

Algorithm

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. For example: [DE](2)HS{P}X(2)PX(2,4)C 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. (Any string of at least 2 characters).

Usage

Command line arguments

Input file format

Pattern specification

The PROSITE pattern definition from the PROSITE documentation follows.

• The standard IUPAC one-letter codes for the amino acids are used.
• The symbol `x' is used for a position where any amino acid is accepted.
• Ambiguities are indicated by listing the acceptable amino acids for a given position, between square parentheses `[ ]'. For example: [ALT] stands for Ala or Leu or Thr.
• Ambiguities are also indicated by listing between a pair of curly brackets `{ }' the amino acids that are not accepted at a given position. For example: {AM} stands for any amino acid except Ala and Met.
• Each element in a pattern is separated from its neighbor by a `-'. (Optional in patmatdb).
• Repetition of an element of the pattern can be indicated by following that element with a numerical value or a numerical range between parenthesis. Examples: x(3) corresponds to x-x-x, x(2,4) corresponds to x-x or x-x-x or x-x-x-x.
• When a pattern is restricted to either the N- or C-terminal of a sequence, that pattern either starts with a `<' symbol or respectively ends with a `>' symbol.
• A period ends the pattern. (Optional in patmatdb).

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

Notes

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

Diagnostic Error Messages

Exit status

Known bugs

Author(s)

History

Target users

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