Rebekah, The reason for this is the way Blast calculates e-values. The e-value is a function of the score. The higher the score, the lower the e-value. The score gets lower as the alignment gets worse and also depends on the length of the query sequence. So, for a lower e-value to be obtained, say 10e-10, the alignment for the HSP must be better than the alignment for the HSP that generates an e-value of 10e-7. If the alignment can be worse, chances are that more of the query sequence will show up in the HSPs, thus creating different output. Also, the e-value is a function of the length of the sequence and the size of the database. So a shorter query sequence that is 10% diverged from the hit will have a higher e-value than a query sequence that is 5 times longer than the short sequence with the same divergence. I hope this helps. Unfortunately, comparing different e-values in Blast can be a little like comparing apples to oranges. I have found that this can be circumvented by using a sliding e-value. You can use this to make sure all query sequences, regardless of length, match a certain criteria, such as at least 50% similarity over the entire length of the query sequence. It gets a little more complicated, but at least it is comparing apples to apples. Thanks, John Pace PhD Candidate University of Texas at Arlington
> Date: Fri, 8 Feb 2008 20:56:41 -0500> From: [EMAIL PROTECTED]> To: > [email protected]> Subject: [BiO BB] Inconsistent Blast Results> > Hi:> > > I'm currently running blast 2.2.14 locally on my mac. I've noticed> that > the printout from a blastn run at an E cutoff of 10^-10 reads> differently > than a blast run at an E cutoff of 10^-7 when hits worse> than 10^-10 are > ignored. Suddenly at 10^-7 new hits with evals of> 10^-11 appear that weren't > there before and even the relative strength> of different hits can change.> > > I'm not certain I understand why this is true and it has a huge impact> on my > results. I know that the Eval is dependent on certain constants> taken from > the compared sequences, but I don't understand how this> could possibly > change when I'm using the exact same input file and> database.> > Does anyone > have an explanation?> > -Rebekah> > > _______________________________________________> BBB mailing list> > [email protected]> http://www.bioinformatics.org/mailman/listinfo/bbb _________________________________________________________________ Climb to the top of the charts! Play the word scramble challenge with star power. http://club.live.com/star_shuffle.aspx?icid=starshuffle_wlmailtextlink_jan _______________________________________________ BBB mailing list [email protected] http://www.bioinformatics.org/mailman/listinfo/bbb
