Question: Conditional reciprocal blast confusion
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gravatar for Biogeek
14 months ago by
Biogeek350
Biogeek350 wrote:

Dear all,

I have 2 assemblies. A de novo assembly and a draft genome assembly of an organism. My aim is to confirm that specific genes of the de novo do in fact appear in the draft genome. I will then design primers around the best match obtained form the CRB analysis.

I am using crb-blast: https://github.com/cboursnell/crb-blast.

If I use the transcriptome as the query, several of the transcriptome genes will obtain a positive hit with the same gene within the genome (for instance, several of my transcripts provide a best CRBB hit to the same genome gene).

If I use the genome as the query, several of the genome genes will obtain a positive hit with the same transcript within the transcriptome.

Can someone please help me understand CRB. I was under the idea that you would end up with a 1 for 1 match, instead several matches are coming up for genes/ transcripts which are queried. I am aware that several transcripts are produced by a gene; however, is the idea of CRB not to ultimately provide a 1 for 1 best match?

If this is the case, how do you choose the best sequence to design the primers around? Do i keep the de novo as the query and the target as the genome? Thanks.

crb-blast • 332 views
ADD COMMENTlink modified 14 months ago • written 14 months ago by Biogeek350
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