fuzztran1e
Search for patterns in protein sequences (translated)
Usage
fuzztran -sequence
seqall
-pattern
pattern
[-frame
list]
[-table
list]
-outfile
report
fuzztran -help
Overview
fuzztran is a command line program from EMBOSS (“the European Molecular Biology Open Software Suite”). It is part of the "Nucleic:Motifs,Protein:Motifs" command group(s).
Options
Input section
-
-sequence seqall
-
-pattern pattern -
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 gven 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). For example, [DE](2)HS{P}X(2)PX(2,4)C
Additional section
-
-frame list -
Default value: 1
-
-table list
Output section
-
-outfile report
Releases
9 releases since Debian 5.0 (Lenny); the text changed 2 times.