transeq | Sequence Analysis in a Nutshell: A Guide to Common Tools and Databases

transeq

transeq translates nucleic acid sequences to the corresponding peptide sequence.

To translate a sequence "pop.seq" in the first frame (starting at the first base and proceeding to the end):

% transeq pop.seq pop.pep

To translate a sequence "pop.seq" in the second frame:

% transeq pop.seq pop.pep -frame=2

To translate a sequence "pop.seq" in the third frame in the reverse sense (starting at the last base and proceeding to the start):

% transeq pop.seq pop.pep -frame=-1

To translate a sequence "pop.seq" in all three forward frames:

% transeq pop.seq pop.pep -frame=F

To translate a sequence "pop.seq" in all three reverse frames:

% transeq pop.seq pop.pep -frame=R

To translate a sequence "pop.seq" in all six forward and reverse frames:

% transeq pop.seq pop.pep -frame=6

To translate a specific set of regions corresponding to a known set of coding sequences:

% transeq pop.seq pop.pep -reg=2-45,67-201,328-509

To translate a sequence "mito.seq" using the mammalian mitochondrion genetic code table:

% transeq mito.seq mito.pep -table=2

Mandatory qualifiers:

[-sequence] (seqall): Sequence database USA.
[-outseq] (seqoutall): Output sequence(s) USA.

Optional qualifiers:

-frame (menu)

Frame(s) to translate.

-table (menu)

Code to use. See the fuzztran description for codes.

-regions (range)

Regions to translate. If this is left blank, the complete sequence is translated. A set of regions is specified by a set of pairs of positions. The positions are integers. They are separated by any non-digit, non-alpha character. Examples of region specifications are:

24-45, 56-78 1:45, 67=99;765..888 1,5,8,10,23,45,57,99

Note: you should not try to use this option with any other frame than the default, -frame=1.

-trim (boolean)

This removes all X and asterisk characters from the right end of the translation. The trimming process starts at the end and continues until the next character is not an X or an asterisk.

Advanced qualifiers:

-alternative (boolean): The default definition of frame -1 is the reverse-complement of the set of codons used in frame 1. (frame -2 is the set of codons used by frame 2, similarly frames -3 is the set used by 3). This is a common standard, used by the Staden package and other programs. If you prefer to define frame -1 as using the set of codons starting with the last codon of the sequence, set this to true.