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  • Alagurajvelu
    Junior Member
    • Apr 2011
    • 6
    #1

    six frame translation

    Hello everyone,
    We have a RNAseq denovo assembly. From these cDNA sequences we want to get the protein sequences. How can i decide which frame translation is correct (out of six frames).
    We thought of taking any frame tranlated sequences which have hits to other known sequences. But we see more than one frame translated proteins hits to known sequences in NCBI.
    If we decide the longest frame, in that cDNA the "ATG" is not there. what should we do here.
    best regards
    Alvel
    Tags: cdna, sixframe, translation
    • Kennels
      Senior Member
      • Feb 2011
      • 149
      #2
      The trinity assembler package has a utility called transdecoder that can extract a best protein set from your assembly for you:

      http://trinityrnaseq.sourceforge.net...anscripts.html

      All you need is your transcripts fasta file as input.

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