[BiO BB] alignment problem

Pankaj pankaj at nii.res.in
Wed Jan 21 03:55:56 EST 2004

hi all,
i have 100 sequences. i want to find the percentage simialrity of
every sequence to every other sequence. ie i want to prepare a 100X100
matrix. i m using local blast from ncbi to find the similarity. but
sometimes the output file from blast has 2 alignments between the
sequences. ie sequence1 with sequence2 has 2 possible alignments (ie
over different parts of the sequences). how do i find the percentage
similarity between the sequences.
if i multipli align these 100 sequences by clustalw, i can see large
gaps in certain regions but i know that all these sequences catalyse
the same reaction. 
thanks in advance

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