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fuzztran - Search for patterns in protein sequences (translated)


fuzztran -sequence seqall -pattern pattern [-frame list] [-table list] -outfile report

fuzztran -help


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).


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

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