Translate nucleotide sequence into AA sequence before BLAST?

Question

[braun_tube]

I have a series of nucleotide assemblies which I want to BLAST search for certain genes. I have the nucleotide fasta files of the genes I want to search for. Is it better practice to just do a nucleotide/nucleotide blast or should I convert the gene files into AA sequences?

Answer 1

[antonioggsousa]

Hi,

Why you don't use the blastx tool, it will translate nucleotide into protein before blasting against a protein database. If the sequences that you are trying to annotated are functional and distant, using blastx would provide better results than just blastn, specially to annotate distant but functional related proteins.

António

[Mensur Dlakic]

If the sequences that you are trying to annotated are functional and distant, using blastx would provide better results than just blastn, specially to annotate distant but functional related proteins.

I don't think that the poster ever wanted to use blastn - the question was about translating the sequences before or during the search. My recommendation is to translate the sequences before the search and use blastp, as that will cut down on time.

[Mensur Dlakic]

My apologies, I see that the issue of using blastn was brought up. Still think it is better to translate ahead of time and use blastp.

[antonioggsousa]

I understand your point.

I'm not sure about what I'll tell next, but I think blastx will try to align the sequences for the 3 possible reading frames. This can be useful in some situations. Though if the author has already the CDS and, the respective ORF, yes, I agree with you, it would be faster following your recommendation.

António