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 <[EMAIL PROTECTED]> 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
