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Can I directly blast mRNAs against nr database or I need to convert it to cds first

Now I have a fasta file of mRNAs (all exons with UTRs) that I hope to annotate. Is it necessary to find the start and stop codon and blast only the CDS region to the NCBI nr database using blastx command-line tool?

rna-seq annotation blast genome
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updated by JC JC • written by tianshenbio tianshenbio

Searches against nr can be very time consuming and if you have a lot of sequences, you may want to do the search locally or switch to diamond v.2 instead.

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written by GenoMax GenoMax

Hi, yes I am actually using the blastx function within diamond.

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written by tianshenbio tianshenbio

1 answer

It is not necessary, BlastX will translate your mRNA to the respective protein. Just be careful for incorrect hits (for example if there are more than one ORF in your sequence)

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written by JC JC

Thank you for your reply. Will give it a try.

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written by tianshenbio tianshenbio

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