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

[Trakhtenberg, F. <Eph...@ch...>]

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...<mailto:Eph...@ch...>> wrote:

Thank you for the clarification. Any recommendations on which tool I could use for predicting polyA?



________________________________
From: Brian Haas [bh...@br...<mailto:bh...@br...>]
Sent: Saturday, July 19, 2014 5:53 PM
To: Trakhtenberg, Feliks
Cc: tra...@li...<mailto: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...<mailto: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