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Old 01-15-2014, 03:09 PM   #1
Junior Member
Location: Valencia, Spain

Join Date: Dec 2013
Posts: 9
Lightbulb Pipeline suggestions for gene detection

Hi everybody!

I've been searching this question through the internet and forum but I didn't find an answer.

I'm working with a non annotated (Scaffold stage) genome (Leptinotarsa decemlineata or Colorado Potato Beetle). I want to know if a receptor from a close specie (Tribolium castaneum) wich is annotated and thus, available in FASTA, is within Colorado Potato Beetle genome. I want to know this because, in that case, I would want to silence it using mRNAi.

So I think the first step is to run a BLAST, wich I already ran, and find if there is homology, wich I found in two scaffolds.

From here, and sorry for bother you with my naive questions, I do not know what to do to finally get a presumptive mRNA(CDS) and/or information about introns and exons.

My actual question is: Can you suggest me any pipeline using the appropriate bioinformatic tools to get that mRNA?

Thank you in advance!
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