EMBOSS: fuzznuc


Program fuzznuc

Function

Nucleic acid pattern search

Description

fuzznuc uses PROSITE style patterns to search nucleotide sequences.

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.

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

Usage

Here is a sample session with fuzznuc.

% fuzznuc
Input sequence: embl:hhtetra
Search pattern: AAGCTT
Number of mismatches [0]: 
Output file [hhtetra.fuzznuc]:

Command line arguments

   Mandatory qualifiers:
  [-sequence]          seqall     Sequence database USA
   -pattern            string     Search pattern
   -mismatch           integer    Number of mismatches
  [-outf]              outfile    Output file name

   Optional qualifiers: (none)
   Advanced qualifiers:
   -mmshow             bool       Show mismatches
   -accshow            bool       Show accession numbers
   -descshow           bool       Show descriptions
   -complement         bool       Search complementary strand


Mandatory qualifiers Allowed values Default
[-sequence]
(Parameter 1)
Sequence database USA Readable sequence(s) Required
-pattern Search pattern Any string is accepted An empty string is accepted
-mismatch Number of mismatches Integer 0 or more 0
[-outf]
(Parameter 2)
Output file name Output file <sequence>.fuzznuc
Optional qualifiers Allowed values Default
(none)
Advanced qualifiers Allowed values Default
-mmshow Show mismatches Yes/No No
-accshow Show accession numbers Yes/No No
-descshow Show descriptions Yes/No No
-complement Search complementary strand Yes/No No

Input file format

Patterns for fuzznuc 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 (amended to refer to nucleic acid sequences, not proteins) follows.

For example, in the EMBL entry ECLAC 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

Here is the output from the example search:


        HHTETRA     1 AAGCTT
        HHTETRA  1267 AAGCTT

It is composed of three columns of data.

If the option '-mmshow' is used, then an extra column of data is output indicating how many mismatches there are in the match, for example:

% fuzznuc embl:hhtetra -mmshow
Nucleic acid pattern search
Search pattern: AAGCTT
Number of mismatches [0]: 1
Output file [hhtetra.fuzznuc]: stdout


        HHTETRA       53     1 AAGCTG
        HHTETRA      140     1 AAGCAT
        HHTETRA      314     1 AACCTT
        HHTETRA      350     1 AAGCCT
        HHTETRA      374     1 AAGTTT
        HHTETRA     1009     1 AAGTTT
        HHTETRA     1259     1 AAGTTT
        HHTETRA     1267     0 AAGCTT

Data files

Notes

References

Warnings

Diagnostic Error Messages

Exit status

Known bugs

See also

Program nameDescription
dregregular expression search of a nucleotide sequence
fuzzproProtein pattern search
fuzztranProtein pattern search after translation
patmatdbSearch a protein sequence with a motif
patmatmotifsSearch a PROSITE motif database with a protein sequence
pregregular expression search of a protein sequence
pscanScans proteins using PRINTS
tfscanScans DNA sequences for transcription factors

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:

Author(s)

This application was written by Alan Bleasby (ableasby@hgmp.mrc.ac.uk)

History

Target users

This program is intended to be used by everyone and everything, from naive users to embedded scripts.

Comments