[modeller_usage] Regarding Usage of BLOSUM Matrix

[Ashish Runthala <ashishr@bits-pilani.ac.in>]

Dear Modellers,
I simply want to study the effect of BLOSUM matrix on the alignment for a different work. 
I want to choose BLOSUM45, BLODSUM80 matrices while computing the pairwise alignment. 
Is there any tool or server, where such feature can be customized before computing the pairwise alignment between a templates' Chain Sequence and a target sequence.

Thanks & Regards,
Ashish

Ashish Runthala,
Lecturer, Structural Biology Cell,
Biological Sciences Group,
BITS, Pilani
Rajasthan, INDIA