Question

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

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4.3 years ago

tianshenbio ▴ 180

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 • 835 views

ADD COMMENT • link updated 4.3 years ago by JC 13k • written 4.3 years ago by tianshenbio ▴ 180

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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.

ADD REPLY • link 4.3 years ago by GenoMax 147k

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

ADD REPLY • link 4.3 years ago by tianshenbio ▴ 180

score 1 · Answer 1 · 2020-08-14

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4.3 years ago

JC 13k

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)