Function

Description

fuzznuc searches for a specified PROSITE-style pattern in nucleotide 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 nucleotide 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 (amended to refer to nucleic acid sequences, not proteins) follows.

• The standard IUPAC one-letter codes for the nucleotides are used.
• The symbol `n' is used for a position where any nucleotide is accepted.
• Ambiguities are indicated by listing the acceptable nucleotides for a given position, between square parentheses `[ ]'. For example: [ACG] stands for A or C or G.
• Ambiguities are also indicated by listing between a pair of curly brackets `{ }' the nucleotides that are not accepted at a given position. For example: {AG} stands for any nucleotides except A and G.
• Each element in a pattern is separated from its neighbor by a `-'. (Optional in fuzznuc).
• 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: N(3) corresponds to N-N-N, N(2,4) corresponds to N-N or N-N-N or N-N-N-N.
• When a pattern is restricted to either the 5' or 3' end of a sequence, that pattern either starts with a `<' symbol or respectively ends with a `>' symbol.
• A period ends the pattern. (Optional in fuzznuc).
• All other characters, including spaces are not allowed.

For example, in the EMBL entry J01636 you can look for the pattern:

[CG](5)TG{A}N(1,5)C

This searches for "C or G" 5 times, followed by T and G, then anything except A, then any base (1 to 5 times) before a C.

You can use ambiguity codes for nucleic acid searches but not within [] or {} as they expand to bracketed counterparts. For example, "s" is expanded to "[GC]" therefore [S] would be expanded to [[GC]] which is illegal.

Note the use of X is reserved for proteins. You must use N for nucleic acids to refer to any base.

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

Output file format

By default fuzznuc 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

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