[BiO BB] alignment problem

[Renyi Liu]

Hi, Pankaj,

Since the number of sequences is not so big, I would use Smith-Waterman 
algorithm to obtain optimal local alignment between any two sequences.

For multiple alignment, I would try T_Coffee or/and Dialign2. Both program 
can be downloaded from the internet, but I am not sure if they can handle 
100 sequences.

Good luck,

Renyi


>From: Pankaj <pankaj at nii.res.in>
>Reply-To: bio_bulletin_board at bioinformatics.org
>To: bio_bulletin_board at bioinformatics.org
>Subject: [BiO BB] alignment problem
>Date: Wed, 21 Jan 2004 14:25:56 +0530 (IST)
>
>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
>pankaj
>
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