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fuzztrane - Online in the Cloud

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This is the command fuzztrane that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator



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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