Stand alone Blast

[magicsiew]

Hi, I have download whole banana EST from GenBank (more than 30,000 EST), then I want to do stand alone blast against my gene of interest collected from other species, but not yet annotated in GenBank. However, after I perform stand alone blast, found no match on my gene of interest. What I want to ask is my method using stand alone blast to find the matching is correct or not? Or stand alone blast can't do that? And do you have any suggestion on other software to use? Thank you... ^^

[JackBean]

I don't think the problem would be in algorithm (stand alone BLAST), but rather in settings or absence of your gene

[magicsiew]

Hi JackBean, thanks.. Ya, is really due to absence of the gene...