fuzztran

fuzztran

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fuzztran uses PROSITE style protein patterns to search nucleic acid sequences translated in the specified frame(s).

Here is a sample session with fuzztran, using all options:

% fuzztran -opt Protein pattern search after translation Input sequence(s): embl:rnops Translation frames          1 : 1          2 : 2          3 : 3          F : Forward three frames         -1 : -1         -2 : -2         -3 : -3          R : Reverse three frames          6 : All six frames Frame(s) to translate [1]: f Genetic codes          0 : Standard          1 : Standard (with alternative initiation codons)          2 : Vertebrate Mitochondrial          3 : Yeast Mitochondrial          4 : Mold, Protozoan, Coelenterate Mitochondrial and Mycoplasma/              Spiroplasma          5 : Invertebrate Mitochondrial          6 : Ciliate Macronuclear and Dasycladacean          9 : Echinoderm Mitochondrial         10 : Euplotid Nuclear         11 : Bacterial         12 : Alternative Yeast Nuclear         13 : Ascidian Mitochondrial         14 : Flatworm Mitochondrial         15 : Blepharisma Macronuclear         16 : Chlorophycean Mitochondrial         21 : Trematode Mitochondrial         22 : Scenedesmus obliquus         23 : Thraustochytrium Mitochondrial Code to use [0]: Search pattern: RA Number of mismatches [0]: Output file [rnops.fuzztran]:

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 fuzztran.)

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 fuzztran.) For example, [DE](2)HS{P}X(2)PX(2,4)C8.

-mismatch (integer)

Number of mismatches.

[-outfile] (report)

Output report filename.

Optional qualifiers:

-frame (menu)

Frame(s) to translate.

-table (menu)

Code to use.