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 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

BUGS

       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.

EMBOSS 6.4.0                                       05/11/2012                                       FUZZTRAN(1e)