perfect alignment match

[NicoBxl]

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

[NicoBxl]

it's strange isn't it ?

nobody knows ?

[epigen]

Blast is a local alignment tool, so it will only consider the aligned part, in you example the ATGC, which is the same in all 3 sequences. There are 4 perfect matches, giving the same score for all 3. The e value is calcuated from the length of the match and the score - also the same. At no point the length of the whole target sequence is taken into account. That means to get your "best alignment" for the same size, you have to filter the results by target sequence length, probably by writing a small script. I don't know of any Blast parameter that could be useful.

[NicoBxl]

ok I'll write a perl script

thanks