Terminology question from a novice

sma · 02-01-2011, 08:11 AM

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!

maubp · 02-01-2011, 02:22 PM

As an aside, why are you not using Newbler 2.5? Reportedly it does a better job, see e.g.
Kumar and Blaxter (2010), http://www.biomedcentral.com/1471-2164/11/571

flxlex · 02-02-2011, 10:49 AM

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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02-01-2011, 08:11 AM	#1
sma Junior Member Location: Hong Kong Join Date: Aug 2010 Posts: 2	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!

02-01-2011, 02:22 PM	#2
maubp 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), http://www.biomedcentral.com/1471-2164/11/571

02-02-2011, 10:49 AM	#3
flxlex Moderator 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'...