Sequence pattern search


fuzzpro/fuzznuc/fuzztran: emboss prosite-style pattern search in amino/nucleic sequences

Fuzz-pro/nuc/tran uses PROSITE style patterns to search protein sequences.
Patterns are specifications of a (typically short) length of sequence to be found. They can specify a search for an exact sequence or they can allow various ambiguities, matches to variable lengths of sequence and repeated subsections of the sequence.

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

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Enter pattern here: (raw text)

Enter sequence to match : (fasta)

or upload a file :

(please make sure the file is in valid fasta format)
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Search type Sequence type on which to perform pattern match on
Frames to use fuzztran specific options
Genetic code fuzztran specific options
Allowed mismatches Fuzz pro/nuc/tran option
Output option Fuzz pro/nuc/tran output option (available :default [custom summary display], excel, gff, pir,trace,dbmotif, feattable, motif, simple, tagseq)
Other common options

Complete Genomes DataBase selection

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Genome list last revision on 2017/08/01:13:17:46

Full Phylogenetic Domain selection: Select full phylogenetic domains or open genomes window to make custom selection

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Taxonomy Name selection: Type valid taxonomy name - Suggested names appear as you type

Matches only full names
(Names for lineages are from NCBI Taxonomy data)
Taxa Tree selection: Browse taxonomy trees . Click on items to open/close nodes or open lineage selections

(Lineage data for tree construction is from NCBI Taxonomy data)

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