Hi, 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. Regards, 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 FRANCE Tel : +262 262 938641 Fax : +262 262 938237 ********************************************************************** ------------------------------------------------- This mail sent through IMP: http://horde.org/imp/