[BiO BB] Inconsistent Blast Results

Martin Gollery marty.gollery at gmail.com
Mon Feb 11 12:28:40 EST 2008

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,

On Feb 8, 2008 5:56 PM, Rebekah Rogers <rebekah.rogers at gmail.com> 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
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Martin Gollery
Senior Bioinformatics Scientist
TimeLogic- a Division of Active Motif
880 Northwood Blvd. Suite 7
Incline Village, NV 89451

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