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fuzznuc - Search for patterns in nucleotide sequences


fuzznuc -sequence seqall -pattern pattern -complement boolean -outfile report

fuzznuc -help


fuzznuc is a command line program from EMBOSS (“the European Molecular Biology Open
Software Suite”). It is part of the "Nucleic:Motifs" command group(s).


Input section
-sequence seqall

-pattern pattern
The standard IUPAC one-letter codes for the nucleotides are used. The symbol 'n' is
used for a position where any nucleotide is accepted. Ambiguities are indicated by
listing the acceptable nucleotides for a given position, between square parentheses '[
]'. For example: [ACG] stands for A or C or G. Ambiguities are also indicated by
listing between a pair of curly brackets '{ }' the nucleotides that are not accepted
at a given position. For example: {AG} stands for any nucleotides except A and G. Each
element in a pattern is separated from its neighbor by a '-'. (Optional in fuzznuc).
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: N(3)
corresponds to N-N-N, N(2,4) corresponds to N-N or N-N-N or N-N-N-N. When a pattern is
restricted to either the 5' or 3' end of a sequence, that pattern either starts with a
'<' symbol or respectively ends with a '>' symbol. A period ends the pattern.
(Optional in fuzznuc). For example, [CG](5)TG{A}N(1,5)C

Advanced section
-complement boolean
Default value: N

Output section
-outfile report

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