TranscriptDecoder and finding ORF

Question

[seta]

Dear all,

Please accept my apologize for asking probably basic question. Could you please let me know whether "TranscriptDecoder" find possible ORF in all 6 reading frames and reported them or it scores all reading frames and report the highest one? I plan to use this tool followed by blastp instead of using blastx that is really time-consuming. However, in this case I'm not sure if output of this pipeline is identical with blastx results and all possible data and information will be maintained. Thanks for sharing your comments and experience.

Answer 1

[Dr Reema Singh]

Hello Seta,

In my view - Yes, Transdecoder finds ORF in all reading frame and report the ORF with greater coding score. I am guessing it after looking at my .pep and .cds file generated by transdecoder. But for confirmation I would suggest you to post your query at Transdecoder google group. Once you get your answer don't forget to comment back.

[seta]

From Brian J, Haas: It reports all ORFs that are considered to be likely coding sequences, not just any single best one

[Dr Reema Singh]

OK Thanks Seta