Re: [Transdecoder-users] Does TranscriptDecoder also predict polyA?
Extracting likely coding regions from transcript sequences
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Re: [Transdecoder-users] Does TranscriptDecoder also predict polyA?
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From: Brian H. <bh...@br...> - 2014-07-23 01:20:33
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It's definitely an interesting research question. We've noticed anecdotally that many of our Trinity-reconstructed transcripts appear to have a stretch of polyA at their 3' end (or in non-strand-specific RNA-Seq assembly, a poly T at 5' end corresponding to the rev-comp). It would be useful to know how many polyA's we can detect, from the reads and from our rna-seq assemblies. Note, we have a polyA-detection system that we used in PASA ( http://pasa.sf.net), and published a couple of papers on several years ago, based on EST and cDNA data, but I haven't revisited it with more modern data types. It's certainly an area that deserves a lot more attention. best, ~b On Tue, Jul 22, 2014 at 9:01 PM, Trakhtenberg, Feliks < Eph...@ch...> wrote: > This may actually be interesting to investigate: what percent of the > transcripts with TranscriptDecoder predicted ORF have polyA site > predicted in appropriate location, and how this correlates with actual > polyA addition. We have polyA-selected RNAseq and total RNAseq (after ribo > depletion), which we could use for addressing this question. Still trying > to figure out if we could also detect actual polyA sequences on 3' RNA > fragments in the raw reads. I am also interested in polyA-lncRNAs, which > have no ORF but are exported to the cytoplasm because of polyA. If these > questions might be of interest to you too, or if this has been done > already, please let us know. > > > thank you, > Ephraim > > > ------------------------------ > *From:* Brian Haas [bh...@br...] > *Sent:* Tuesday, July 22, 2014 1:17 PM > *To:* Trakhtenberg, Feliks > *Cc:* tra...@li...; rc...@li... > > *Subject:* Re: [Transdecoder-users] Does TranscriptDecoder also predict > polyA? > > 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 >>>> >>>> >>>> ------------------------------------------------------------------------------ >>>> Want fast and easy access to all the code in your enterprise? Index and >>>> search up to 200,000 lines of code with a free copy of Black Duck >>>> Code Sight - the same software that powers the world's largest code >>>> search on Ohloh, the Black Duck Open Hub! Try it now. >>>> http://p.sf.net/sfu/bds >>>> _______________________________________________ >>>> Transdecoder-users mailing list >>>> Tra...@li... >>>> https://lists.sourceforge.net/lists/listinfo/transdecoder-users >>>> >>>> >>> >>> >>> -- >>> -- >>> 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 > > > -- -- Brian J. Haas The Broad Institute http://broad.mit.edu/~bhaas |
