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

[Martin M. <mmo...@gm...>]

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