Getting all translated ORFs from 6 frame not just longest ones

Question

[seta]

Dear all,

Could you please introduce me a tool, which can give me all translated ORF resulting from 6 frame not just longest ORF?. As far as I know most ORF prediction tool, like Transcript decoder, ORF Finder reports just longest ORF. We are dealing with computational prediction and longest ORF is not always the best and true one (true ORF just determined with experimental task). I plan to retrieve all translated ORF in 6 frames followed by doing blastp instead of using blastx. Thanks for all your help

[jinxyhucy521]

Dear seta,I have also faced this problem,and it has pullzed me a lot ,could you help me how to solve this problem??And I hope to get help from you .

[seta]

You can use TransDecoder enter link description here. I was satisfied with it.

Answer 1

[Pierre Lindenbaum]

http://emboss.sourceforge.net/apps/cvs/emboss/apps/transeq.html

transeq reads one or more nucleotide sequences and writes the corresponding protein sequence translations to file. It can translate in any of the 3 forward or three reverse sense frames, or in all three forward or reverse frames, or in all six frames. The translation may be restricted to specified regions, for example, corresponding to the coding regions of your sequences. It can translate using the standard ('Universal') genetic code and also with a selection of non-standard codes.

[seta]

Thanks Pierre. Would you please just let me know if it will work well on assembled transcriptome file, containing about 40000 sequence?

Answer 2

[x.jack.min]

the orfpredictor will do the job for you -- for all 6 frames