This is the command fuzzproe 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
PROGRAM:
NAME
fuzzpro - Search for patterns in protein sequences
SYNOPSIS
fuzzpro -sequence seqall -pattern pattern -outfile report
fuzzpro -help
DESCRIPTION
fuzzpro is a command line program from EMBOSS (“the European Molecular Biology Open
Software Suite”). It is part of the "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 given 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
fuzzpro). 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 fuzzpro). For example, [DE](2)HS{P}X(2)PX(2,4)C
Output section
-outfile report
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