fuzznuc1e
Search for patterns in nucleotide sequences
Usage
fuzznuc -sequence
seqall
-pattern
pattern
-complement
boolean
-outfile
report
fuzznuc -help
Overview
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).
Options
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
Releases
9 releases since Debian 5.0 (Lenny); the text changed 2 times.