[BiO BB] Inconsistent Blast Results

[Mike Marchywka]

>> 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. 



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> Date: Mon, 11 Feb 2008 09:28:40 -0800
> From: marty.gollery at gmail.com
> To: bbb at bioinformatics.org
> 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
>>
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>>
>
>
>
> --
> --
> Martin Gollery
> Senior Bioinformatics Scientist
> TimeLogic- a Division of Active Motif
> 775-833-9113
> 880 Northwood Blvd. Suite 7
> Incline Village, NV 89451
>
> _______________________________________________
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> http://www.bioinformatics.org/mailman/listinfo/bbb

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