[ssml] 4 different results from BLAST using blosum62 & 50.

Manoj Tyagi Manoj.TYAGI at univ-reunion.fr
Thu Aug 26 03:15:16 EDT 2004

I wanted to use my own matrix in Blast and tried blastall -M "matrix file" 
option but Blast says only few matrices are supported. I wrote to NCBI and got 
anwser that rename my matrix to BLosum62 & it would work. yes this option makes 
blast to accept the matrix but I had real doubts on results.
So to verify I did small test I took blosum62 & blosum50 matrix generated 
resutls from them then I renamed each vice versa & again did blast, to my 
surprise results were completly different. I got 4 different results using only 
2 matrices. 
Could anyone one of you explain why we are getting such results? 

My intuition says BLAST has been hard coded with matrix information which imply 
that we can't use user defined matrix with BLAST. 
Looking for your answers. 


Manoj Tyagi

 Manoj TYAGI 
 Laboratoire de Biochimie et Génétique Moléculaire
 Université de La Réunion
 BP 7151, 15 avenue René Cassin
 97715 Saint Denis Messag Cedex 09
 La Réunion
 Tel : +262 262 938641
 Fax : +262 262 938237

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