Entering edit mode
2.8 years ago
v.shapovalova1 ▴ 10
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
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.
Seems that it could be so easy) Thank you, I'll stop searching for a magic flag.
First, I do not know if it works because I have not tried it before. The way is that;
-qcov_hsp_percparameter, at least over 70%, 80%
If it works, let me know :)
Thank you for your reply, but i need different thersholds for identity for different genes, so i've done a lot of repeats.