fuzztran

Function

Description

fuzztran searches for a specified PROSITE-style pattern in nucleic acid sequences that are first translated to protein in the specified frame(s) with a specified genetic code. 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.

Usage

Command line arguments


Input file format

fuzztran reads in normal nucleic acid sequence USAs.

Pattern specification

Patterns for fuzztran 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, 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 fuzztran writes a 'table' report file.

The columns of data are as follows:

  1. Start - the start position of the pattern in the nucleic acids sequence.
  2. End - the end position of the pattern in the nucleic acids sequence.
  3. Score - the score of the match.
  4. Mismatch - the number of mismatches .
  5. Frame - the translation frame that the pattern match occurs in.
  6. PStart - the start position of the match in the resulting protein sequence.
  7. PEnd - the end position of the match in the resulting protein sequence.
  8. Translation - the protein sequence that is matched.

Data files

Notes

None.

References

None.

Warnings

When translating using non-standard genetic code table, always check the table carefully for deviations from your particular organism's code.

Diagnostic Error Messages

None.

Exit status

It always exits with status 0.

Known bugs

None.

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)

History

Target users

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