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Old 02-01-2011, 08:11 AM   #1
Junior Member
Location: Hong Kong

Join Date: Aug 2010
Posts: 2
Default Terminology question from a novice

Hi all,

My lab has recently started using 454 GS FLX titanium pyroseqeuncing of cDNAs for several transcriptome projects with non-model organisms. All of our data has been assembled by Newbler 2.3 and later annotated by search against BLASTx nr database.

We are debating how we should refer to the assembled "isogroups" in our paper. Is appropriate to refer to an "isogroup" as a gene? Or a 'gene'? What about a isotigs or contigs that are not assembled into isogroups but are annotated?

Thanks for you help!
sma is offline   Reply With Quote
Old 02-01-2011, 02:22 PM   #2
Peter (Biopython etc)
Location: Dundee, Scotland, UK

Join Date: Jul 2009
Posts: 1,543

As an aside, why are you not using Newbler 2.5? Reportedly it does a better job, see e.g.
Kumar and Blaxter (2010),
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Old 02-02-2011, 10:49 AM   #3
Location: Oslo, Norway

Join Date: Nov 2008
Posts: 415

I guess the best thing would be to annotate all sequences and cluster them into gene families (or this in reverse order) before calling any two different sequences two different genes or 'genes'...
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