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Old 10-06-2010, 05:05 AM   #1
NicoBxl
not just another member
 
Location: Belgium

Join Date: Aug 2010
Posts: 264
Default perfect alignment match

Hi,

I've a little problem with an alignment. I want to know to view the perfect alignment of a query to a database . Here's an example :

query

>query1
ATGC

subject :

>seq1
GATGC
>seq2
CGATGC
>seq3
ATGC

When I use Blast, the three alignment have the same e-value and score, but the best alignment for me is with seq3 ( same size )

is it a blast parameter to change ?

or an another program to use

Thanks,

Nicolas
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