Question: How can i run a local blastn on my denovo assemble (rnaseq data) for detection known gene?
gravatar for pr.khavari
23 months ago by
Iran, Tehran, University of tehran
pr.khavari0 wrote:

Hi everyone, I have a denovo assemble by Trinity assembler. I want to find some known gene from databases like NCBI and others in order to detect the similarity or homology search from my transcriptome assemble. Do you know an online aligner or command line software? I know the NCBI blast command line but it is a little complex at this time for me. thanks.

rna-seq alignment assembly gene • 440 views
ADD COMMENTlink written 23 months ago by pr.khavari0

Instead of doing blast at this step you should first do a TransDecoder analysis on your data. You could extend that analysis to do pfam search. @h.mon recently provided an answer for protein domain searches that you will find useful : A: How to build a local Pfam database?

Ideally then you could then do DIAMOND alignments against nr database. This does require significant computer resources though.

ADD REPLYlink modified 23 months ago • written 23 months ago by genomax85k

Personally, I'd stick to the the swissprot database. NR isn't curated and will lead to a high proportion of misleading or meaningless annotations.

ADD REPLYlink modified 23 months ago • written 23 months ago by Andy20
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