Re: [Transdecoder-users] Using BLASTN evidence for CDS predictions

[<Ale...@cs...>]

Hi Martin


>Yes, I don't mind it would resurrected mistakenly truly dead genes (pseudogenes).
I think that might be a bit out of the scope of the TransDecoder program as a lot of people would mind. Creating a second software that uses the TransDecoder output and the transcriptome assembly sounds like a better way to do it.

a

________________________________________
From: Martin MOKREJŠ [mmo...@gm...]
Sent: Tuesday, 24 June 2014 11:11 PM
To: tra...@li...
Subject: Re: [Transdecoder-users] Using BLASTN evidence for CDS predictions

Martin MOKREJŠ wrote:
> Hi,
>   I wonder whether TransDecoder could also run blastn against a somewhat related genome/transcriptome
> and considered the matching regions. They will be matching exons and the UTRs won't be conserved.
>
>   Further, could TransDecoder ignore a STOP codon and merge two ORFs if the macthes are in adjacent
> frames on the same target strand?

Aha, forgot to explain a bit more: the alignment to DNA will reveal gaps in either strand so quite helpful
hint for an artificial insertion/deletion. It should be easy for TransDecoder to realize that at that position
is likely an error. Yes, I don't mind it would resurrected mistakenly truly dead genes (pseudogenes).

Martin

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