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Andreas
Oct 7, 2013, 6:22:31 AM10/7/13
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I selected a few related genomes to perform protein BLAST, looking for how well conserved certain proteins were within a family. Puzzled by the lack of results from a few of the genomes, I tried searching with a protein sequence from a genome I hadn't seen any hits in, and this again produces no hits in the genome containing the 100% identity hit. This seems be observed with any protein sequence from Desulfobulbus japonicus, BLAST'ed against the itself (blastp).
It doesn't produce a "not hits found" or even any text at all - just a blank line on the result page.
Using tblastn seems to bypass the problem and I'm able to get the results I expect, but I can't see why it shouldn't work with a normal protein BLAST. Am I doing something wrong or is it a bug?
It doesn't produce a "not hits found" or even any text at all - just a blank line on the result page.
Using tblastn seems to bypass the problem and I'm able to get the results I expect, but I can't see why it shouldn't work with a normal protein BLAST. Am I doing something wrong or is it a bug?
Cara Fiore
Mar 4, 2014, 5:43:23 PM3/4/14
to img-use...@lbl.gov
I also have a similar question - I have tried to BLAST against specific genomes that I highlight using the IMG tool, and when I copy in a sequence that I expect to match the most I get is ~35 bp alignment. Is there a better way to do this, am I doing something wrong?
Also, it would be nice if it says where in the genome the alignment is to - gene ID or something - is it there and I missed it?
Thank you,
Cara
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