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

Question

[tianshenbio]

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?

[GenoMax]

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.

[tianshenbio]

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

Answer 1

[JC]

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)

[tianshenbio]

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