Sequence alignment

Ulrik Ulriks at ruc.dk
Sat Oct 14 07:42:06 EST 2000

Hi all

I am a third year molecular biology student (only just started on my third
year), and I am writing on a project compiling the litterature on a family
of proteins called connexins.

I have found only few comparisons between genes coding for the same protein,
but from different animals. The promotor sequence of one proteine seems to
be very interesting since it seems to differ greatly from animal to animal,
though there is a very high degree of homology between exons and introns.

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.

Is it possible to define a starting point for alignmentsqeuences which has
the first priority in alignment in ClustalW? I'm thinking sequences such as
ATG and TATA. Or to force the alignment of basepair numbers (bp 235 of
sequence A must be aligned with bp 890 of sequence B)?

Another problem of mine, is how to see where sequences start to diverge. It
has been reported that the promotor region from -1 to -120 shows a 90%
similarity between human and rat, but -121 to -800 only shows a similarity
of 62%. I'm looking for an easy way to see this, doea any of you know of a
programme that can help one in such matters, apart form the eye? The dot
plot seems
like a step in the right direction, but I cannot seem to extract any useful
information from the plot.

I have also asked my advisor, but he seems reluctant to answer certain

Thanks for Your help
Ulrik Stervbo

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