Local BLAST search

Question

[v.shapovalova1]

Hello,

I plan to make blast db and find sequences with two genes. So the sequences must have both two genes.(AND AND) Not only the first or only the second.(OR) There is a flag -query in local blast where I'll put genes in fasta format like this:

1 ATGGGGCC.. 2 ATGTTGC..

When I tried to do this I had sequences with the only first gene, the only second gene and the first and the second. How could I filter the variants with both two genes?

A lot of thanks, Valery

[Joe]

You can't do that with blast.

You would need to run 2 separate blast searches, one for each input sequence, and find the commonalities in the outputs.

[v.shapovalova1]

Seems that it could be so easy) Thank you, I'll stop searching for a magic flag.

[young_bioinformatician]

First, I do not know if it works because I have not tried it before. The way is that;

• concatenate the genes - do not write any ids between them
• run blast using -qcov_hsp_perc parameter, at least over 70%, 80%
• check query coverage and/or match position in the results If you know the length of gene you have

If it works, let me know :)

[v.shapovalova1]

Thank you for your reply, but i need different thersholds for identity for different genes, so i've done a lot of repeats.