Function

Description

fuzznuc searches for a specified PROSITE-style pattern in protein sequences. Such patterns are specifications of a (typically short) length of sequence to be found. They can specify a search for an exact sequence or they can allow various ambiguities, matches to variable lengths of sequence and repeated subsections of the sequence. One or more protein sequences are read from file. The output is a standard EMBOSS report file that includes data such as location and score of any matches.

Algorithm

fuzznuc intelligently selects the optimum searching algorithm to use, depending on the complexity of the search pattern specified.

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 fuzzpro).
• 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 fuzzpro).
• All other characters, including spaces are not allowed.

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 fuzzpro writes a 'seqtable' report file.

Data files

Notes

References

Warnings

Diagnostic Error Messages

Exit status

Known bugs

Other EMBOSS programs allow you to search for regular expression patterns but may be less easy for the user who has never used regular expressions before:

• dreg - Regular expression search of a nucleotide sequence
• preg - Regular expression search of a protein sequence

Author(s)

History

Target users

Comments