Sequence alignment

Daniel Nilsson daniel.nilsson at
Tue Oct 24 07:51:35 EST 2000

> I am trying to align different sequences from the genebank. The best program
> I've found so far is BioEdit (Im using PC - Windows or Linux), which uses
> ClustalW to align sequences. I've managed to align two sequences (one of 930
> bp, theother of 2220 bp) with ClustalW, which has been aligned in an
> article, but the only way I could make my alignment look like the alignment
> in the article was if I deleted the sequences before a TATA-box. If i didn't
> do the deletion, neither the exons nor introns would match.

If you are considering the comparison of two, relatively short sequences
I recommend using an implementation of the Smith-Waterman alignment algorithm.
For instance, you could use the swat program that comes with the Phrap/phred
package that Phil Green provides ( or why not the ssearch
program from the good old Bill Pearson FASTA package

It would also be worth considering what program the authors of the article you
compare your results to have used; clustalw or some other program? Are there
many sequences aligned in the same picture? In that case, a multiple alignment
technique has been used. A pairwise comparison will not give you the same

Good luck!

// Daniel Nilsson

Daniel Nilsson
Sysadmin and student
Dept. of Genetics and Pathlogy, Uppsala University
Mail:   daniel.nilsson at
Phone:  +46(0)18 6111077
Snail:  IGP, Rudbeckaboratoriet, 75185 Uppsala

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