FUZZTRAN(1e) | EMBOSS Manual for Debian | FUZZTRAN(1e) |
NAME¶
fuzztran - Search for patterns in protein sequences (translated)SYNOPSIS¶
fuzztran -sequence seqall
-pattern pattern
[-frame list] [
-table list]
-outfile report
fuzztran -help
DESCRIPTION¶
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 patternThe 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 listDefault value: 1
-table list
Output section¶
-outfile reportBUGS¶
Bugs can be reported to the Debian Bug Tracking system (http://bugs.debian.org/emboss), or directly to the EMBOSS developers (http://sourceforge.net/tracker/?group_id=93650&atid=605031).SEE ALSO¶
fuzztran is fully documented via the tfm(1) system.AUTHOR¶
Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>Wrote the script used to autogenerate this manual
page.
COPYRIGHT¶
This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package. It can be redistributed under the same terms as EMBOSS itself.05/11/2012 | EMBOSS 6.4.0 |