protein coding region of transcript assembled by reference

[the_august]

Hello All,

I've got some sequences of RNA transcript made by 454 sequencing and assembled using sequences from a reference genome. I have the sequence of the transcript and the corresponding GenBank ID of the sequence used for its assembly.

How I can predict the protein coding sequence of the transcript. Do I need to align them to the reference sequence first? Is there any particular protocol that people follow? Are there any software tools for doing this? I'm conversant in programming so can do some coding if necessary.

In all probability the sequences contain some frameshift errors. So any remedial method is much appreciated.


Many Thanks

[Kennels]

I'm also interested in the methodologies people use, but here is something I've just started trying, although I'm not sure what to do after such a step:

http://trinityrnaseq.sourceforge.net/analysis/extract_proteins_from_trinity_transcripts.html

[the_august]

Hi Kennels,

I guess the trinity method you've described is to get transcript for De-novo assembled sequences.

I'm looking for methods that can predict protein coding regions from reference sequence guided assembled transcript.

Thanks

[Kennels]

Hi
Actually, it predicts all 6 frames ORFs and selects the best based on the methodology described. You end up with a file with protein sequences, and you can also manipulate what sort of output you want. It does this with assembled transcript sequences as the input, but the situation is analogous to what you are trying to do, unless I understood your problem wrongly.