transdecoder-users

[Transdecoder-users] Using BLASTN evidence for CDS predictions

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

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?

At least ideas for the future,
Martin

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

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

------------------------------------------------------------------------------
Open source business process management suite built on Java and Eclipse
Turn processes into business applications with Bonita BPM Community Edition
Quickly connect people, data, and systems into organized workflows
Winner of BOSSIE, CODIE, OW2 and Gartner awards
http://p.sf.net/sfu/Bonitasoft
_______________________________________________
Transdecoder-users mailing list
Tra...@li...
https://lists.sourceforge.net/lists/listinfo/transdecoder-users

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

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

Hi Alexie,
  hmm, I thought it is calling BLASTP already. I don't think it is worth to come up with yet another
package but I understand your reasonings.
Best,
Martin

Ale...@cs... wrote:
> 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