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 one or more nucleotide sequences.
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.
-
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 fuzztran).
-
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 fuzztran).
- All other characters, including spaces are not allowed.
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:
- Start - the start position of the pattern in the nucleic acids sequence.
- End - the end position of the pattern in the nucleic acids sequence.
- Score - the score of the match.
- Mismatch - the number of mismatches .
- Frame - the translation frame that the pattern match occurs in.
- PStart - the start position of the match in the resulting protein sequence.
- PEnd - the end position of the match in the resulting protein sequence.
- 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.
Author(s)
History
Target users
Comments