transeqe - Online in the Cloud

PROGRAM:

NAME

transeq - Translate nucleic acid sequences

SYNOPSIS

transeq -sequence seqall [-frame list] [-table list] [-regions range] [-trim boolean]
[-clean boolean] -alternative boolean -outseq seqoutall

transeq -help

DESCRIPTION

transeq is a command line program from EMBOSS (“the European Molecular Biology Open
Software Suite”). It is part of the "Nucleic:Translation" command group(s).

OPTIONS

Input section
-sequence seqall

Additional section
-frame list
Default value: 1

-table list

-regions range
Regions to translate. If this is left blank, then 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 '*' characters from the right end of the translation. The
trimming process starts at the end and continues until the next character is not a 'X'
or a '*' Default value: N

-clean boolean
This changes all STOP codon positions from the '*' character to 'X' (an unknown
residue). This is useful because some programs will not accept protein sequences with
'*' characters in them. Default value: N

Advanced section
-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
and 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, then set this to be true. Default value: N

Output section
-outseq seqoutall

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