I'm writing this from the computer lab in the botany wing of biosci waiting for my lab to start. We're going to be down here trying to determine what gene our original cDNA came from and what organism it belongs to. I thought Id go ahead and try it out myself before the lab begins but Im running into some problems.
I aligned my sequences last week but I was a little wary of the results because my sequencing reactions didnt work out all that well. The chromatograms showed a really weak signal all around so it was tough, if not impossible, to determine the correct bases where I got a string of N's. This meant that alot of spots in my sequence were really unknown. The resulting consesus sequence was a little suspect because of this.
I saved the consensus sequence anyway and used it to run a Blast search on NCBI. I should have been able to figure out what the gene was (I know its a form of actin but what form of actin?) and the organism it came from. Except, this didnt happen. I have a whole schwack of results, and about 10 of them all have the same Query coverage, total score, max score, E-value and max identity. Unfoturnately, theyre all from different organisms so I dont know which one is the "right" one. The query coverage and max identity are 83%, which means that my sequence is about 83% identical to these sequences...which isnt all that great. If my sequence was the same as a sequence in the database, then the values should be like 95% or more. This means one of two possible things: either the sequence isnt in the database and the closest thing to it is only 83% identical or my sequence is wrong. I think the latter is more likely. They all are beta-actin genes, though, so at least this tells me my gene is probably a beta actin.