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.