Hi,
I'm trying to blast(x) some contigs I've created. The problem is I have a ton of them so I'd like to reduce the search space by using a database of only viral sequences. I created a database like this, but the results seem off. For example, when I get a sequence that matches with a plant virus, taking that sequence and using NCBI's web blast interface against NR returns plant sequences.
My thinking is that blast returns whatever sequences the query is close to, and when checking against viruses there are only viral sequences so it returns whatever viral sequences there are. When I take the sequence to NR, there are many plant sequences that are much closer so it returns those. Hopefully that makes sense.
The main problem with this is that I can't trust my results. If I get a virus that I'm interested in after searching the viral database, I have to use NR to make sure that it's actually correct. So my question is, can I do anything to make sure when I'm searching against the viral database my results are actually accurate?
I'm trying to blast(x) some contigs I've created. The problem is I have a ton of them so I'd like to reduce the search space by using a database of only viral sequences. I created a database like this, but the results seem off. For example, when I get a sequence that matches with a plant virus, taking that sequence and using NCBI's web blast interface against NR returns plant sequences.
My thinking is that blast returns whatever sequences the query is close to, and when checking against viruses there are only viral sequences so it returns whatever viral sequences there are. When I take the sequence to NR, there are many plant sequences that are much closer so it returns those. Hopefully that makes sense.
The main problem with this is that I can't trust my results. If I get a virus that I'm interested in after searching the viral database, I have to use NR to make sure that it's actually correct. So my question is, can I do anything to make sure when I'm searching against the viral database my results are actually accurate?
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