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Standalone Blast tool and command

how to use standalone blast with assembled RNA data and sequenced peptide.

I have the assembled RNA data and i also have the protein peptides which is sequenced. Can i do standalone blast with the assembled to peptides.

alignment

Yes, you can do a blastx

I see now you are also asking for the command. It looks like something like this:

makeblastdb -in yourprotein.fa -dbtype prot
blastx -query yournucseqs.fa -db yourprotein.fa -out output

With the command blastx -help and blastx --help you can see all the options

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