>> 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 think someone else suggested using the score not the e-value. I'd seen cases using a blast server where I got confusing results so I just got in the habit of asking for a lot of marginal hits and then sort them out locally with text scripts. Mike Marchywka 586 Saint James Walk Marietta GA 30067-7165 404-788-1216 (C)<- leave message 989-348-4796 (P)<- emergency only [EMAIL PROTECTED] Note: Hotmail is blocking my mom's entire ISP claiming it is to reduce spam but probably to force users to use hotmail. Please DON'T assume I am ignoring you and try me on [EMAIL PROTECTED] if no reply here. Thanks. > Date: Mon, 11 Feb 2008 09:28:40 -0800 > From: [EMAIL PROTECTED] > To: [email protected] > Subject: Re: [BiO BB] Inconsistent Blast Results > > Hi Rebekah, > I believe you are seeing differences because of scores getting thrown > out at an earlier step. What I think is happening is that the hits are > being cut off with the 10^-10 threshold that would have given better > results in the alignment regeneration phase. Then when you run the > search with the 10^-7 cutoff, those hits are allowed into the final > step and they are extended to yield better scores. > > Best Regards, > Marty > > On Feb 8, 2008 5:56 PM, Rebekah Rogers wrote: >> 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 >> > > > > -- > -- > Martin Gollery > Senior Bioinformatics Scientist > TimeLogic- a Division of Active Motif > 775-833-9113 > 880 Northwood Blvd. Suite 7 > Incline Village, NV 89451 > > _______________________________________________ > BBB mailing list > [email protected] > http://www.bioinformatics.org/mailman/listinfo/bbb _________________________________________________________________ Helping your favorite cause is as easy as instant messaging. You IM, we give. http://im.live.com/Messenger/IM/Home/?source=text_hotmail_join _______________________________________________ BBB mailing list [email protected] http://www.bioinformatics.org/mailman/listinfo/bbb
