Translate

Description

This tool translate nucleic acid sequences into protein sequences.

Parameters

  • Frame(s) to translate
  • Genetic code to use
  • Regions to translate (eg: 4-57,78-94) Regions to translate. A set of regions is specified by a set of pairs of positions. 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 trailing X's and *'sb 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 '*'
  • Change all *'s to X's 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.
  • Define frame '-1' as starting in the last codon 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.)
  • Output sequence format
  • Details

    This tools runs EMBOSS command transeq to translate the given nucleotide sequence into protein. The input sequences can be in any of the EMBOSS compatible sequence formats.

    Output

    Output is a fasta formatted protein sequence file.