Re: [Transdecoder-users] Does TranscriptDecoder also predict polyA?

[Brian H. <bh...@br...>]

Thanks for the info!

I've been thinking about this some more, and I'm not sure how useful it
will be in the context of transdecoder after all...  This is because,
although these tools can be quite useful for identifying or predicting
sites of polyadenylation, not finding such a site might not be a robust
indicator that you don't have a coding transcript, particularly if you find
a nice long ORF with good coding potential.  For now, I think we'll rely on
coding metrics and homology data, and eventually we'll leverage a lincRNA
and other ncRNA classification tools to facilitate transcriptome
annotations.

best,

~brian



On Tue, Jul 22, 2014 at 12:30 PM, Trakhtenberg, Feliks <
Eph...@ch...> wrote:

>  Hi Brian,
>
>
>
> CC'ed: Lingsheng Dong from our bioinformatics support team.
>
>
>
> The 3 links below seem to offer free software for mouse polyA prediction
> using transcripts sequences input, which could be taken directly from
> Cufflinks de novo transcripts output. I wonder if one of them could be a
> good fit for using along with the TranscriptDecoder. For example, the polyA
> site that occurs on 3' past the predicted stop codon would be valid, but if
> there is no polyA site, or more than 10 bp before the stop codon, such
> transcript would probably not produce a protein even if ORF is predicted.
> The 3' ends are cleaved off about 10 bp downstream of the polyA site prior
> to polyA addition, that is why I thought polyA site could not be more than
> 10 bp upstream of the stop codon. Please let me know what you think about
> this.
>
>
>
> http://exon.umdnj.edu/polya_svm_server/index.html
>  http://mlkd.csd.auth.gr/PolyA/datasets.html
>  http://genes.mit.edu/GENSCAN.html
>
>  Thank you,
>
> Ephraim
>
>
>
> P.S. Links below seem to be either only for Human or predict polyA site
> directly from genome DNA rather than from spliced transcripts sequences:
> http://grail.lsd.ornl.gov/grailexp/
> http://linux1.softberry.com/berry.phtml?topic=products
>  http://www.imtech.res.in/raghava/polyapred/help.html
> http://cbrc.kaust.edu.sa/dps/
> http://dnafsminer.bic.nus.edu.sg/PolyA.html
> http://cub.comsats.edu.pk/polyapredict.htm
>
>
>  ------------------------------
> *From:* Brian Haas [bh...@br...]
> *Sent:* Saturday, July 19, 2014 6:33 PM
>
> *To:* Trakhtenberg, Feliks
> *Cc:* tra...@li...
> *Subject:* Re: [Transdecoder-users] Does TranscriptDecoder also predict
> polyA?
>
>   I actually haven't researched that in a while.  Please let me know if
> you find something really useful.
>
>  best,
>
>  ~brian
>
>
>
> On Sat, Jul 19, 2014 at 6:00 PM, Trakhtenberg, Feliks <
> Eph...@ch...> wrote:
>
>>  Thank you for the clarification. Any recommendations on which tool I
>> could use for predicting polyA?
>>
>>
>>  ------------------------------
>> *From:* Brian Haas [bh...@br...]
>> *Sent:* Saturday, July 19, 2014 5:53 PM
>> *To:* Trakhtenberg, Feliks
>> *Cc:* tra...@li...
>> *Subject:* Re: [Transdecoder-users] Does TranscriptDecoder also predict
>> polyA?
>>
>>    Hi,
>>
>>  TransDecoder does not take into account whether a transcript is
>> polyadenylated or not. It strictly looks at open reading frames and coding
>> potential.
>>
>>  best,
>>
>>  ~brian
>>
>>
>>
>> On Sat, Jul 19, 2014 at 2:38 PM, Trakhtenberg, Feliks <
>> Eph...@ch...> wrote:
>>
>>>  Hello, I am new to TranscriptDecoder. Does it consider whether a novel
>>> transcript with a predicted ORF is also predicted to be polyadenylated?
>>> I assumed if no polyA can be predicted, then even if ORF is predicted,
>>> such transcript may not produce a protein. My input is a group of novel
>>> transcripts predicted by Cufflinks analysis. Would appreciate feedback.
>>> thank you
>>>
>>>
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>>
>>
>>  --
>> --
>> Brian J. Haas
>> The Broad Institute
>> http://broad.mit.edu/~bhaas
>>
>>
>>
>
>
>
>  --
> --
> Brian J. Haas
> The Broad Institute
> http://broad.mit.edu/~bhaas
>
>
>



-- 
--
Brian J. Haas
The Broad Institute
http://broad.mit.edu/~bhaas