Marty (or anyone), Perhaps you can explain this to me. I searched an AA string against the rat genome. I got a poor hit (e-value about 50), so I decided to see if there was a homologous gene, and I searched against all genomes. Instead of returning the same hit (or better), but best hit I received was about 360! Why is this? I'm confounded. Thanks for your help. Dave -----Original Message----- From: biodevelopers-bounces+dangulo=cti.depaul.edu at bioinformatics.org on behalf of Martin Gollery Sent: Wed 1/17/2007 5:23 PM To: Development in Bioinformatics Subject: Re: [Biodevelopers] Blast not symmetrical? This is correct, BLAST is not symmetrical. Some assume that it is and make some pretty serious mistakes. Switch to Smith-Waterman and you will eliminate this problem. Marty On 1/17/07, Michael Nuhn <nuhn at rhrk.uni-kl.de> wrote: > Hello, Everybody! > > While I was trying to track down a "bug" in my program I found out that the > blast program (Blastn v2.2.11) is not symmetrical, that is: > > If I blast a query sequence Q against a database S (1 sequence), I get a > result set B(S,Q). > > If I do the blast the other way around, that is, I use S as query sequence > and blast it against the database Q, I get a result B(Q,S). > > And the problem is: B(S,Q) and B(Q,S) are not equal. Each blast set has some > blast hits that the other does not have and also some blast hits that have > one common coordinate but end at another. > > Both blasts were made with the blast defaults, no filter was used. The two > sequences are large (~2Mb each, the sequences are genomes). According to the > statistics used in blast (at least the part I understand), it should not > play a role which sequence is the query and which is the subject. > > Does anyone have an explanation for this? Since I don't really have a clue > at where to start, hints and wild guesses are also appreciated. > > Thanks in advance, > Michael. > > _______________________________________________ > Biodevelopers mailing list > Biodevelopers at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/biodevelopers > -- -- Martin Gollery Associate Director Center For Bioinformatics University of Nevada at Reno Dept. of Biochemistry / MS334 775-784-7042 ----------- _______________________________________________ Biodevelopers mailing list Biodevelopers at bioinformatics.org https://bioinformatics.org/mailman/listinfo/biodevelopers