fuzznuc

fuzznuc

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fuzznuc uses PROSITE style patterns to search nucleotide sequences.

Here is a sample session with fuzznuc:

% fuzznuc Input sequence: embl:hhtetra Search pattern: AAGCTT Number of mismatches [0]: Output file [hhtetra.fuzznuc]:

Mandatory qualifiers:

[-sequence] (seqall)

Sequence database USA.

-pattern (string)

The standard IUPAC one-letter codes for the amino acids are used. The letter 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 brackets. For example, [ALT] stands for Ala, Leu, or Thr. Ambiguities are also indicated by listing the amino acids that are not accepted at a given position in curly brackets. For example, {AM} stands for any amino acid except Ala and Met. Each element in a pattern is separated from its neighbor by a dash. (Optional in fuzznuc.)

Repetition of an element of the pattern is indicated by following that element with a numerical value or a numerical range between parenthesis. For example, x(3) corresponds to x-x-x, while x(2,4) corresponds to x-x, 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 ends with a ">" symbol, respectively. A period ends the pattern. (Optional in fuzznuc.) For example, [DE](2)HS{P}X(2)PX(2,4)C8.

-mismatch (integer)

Number of mismatches.

[-outfile] (report)

Output report filename.

Advanced qualifiers:

-complement (boolean)

Search complementary strand.