Sequence comparison

[Shigenari Hayashi]

In <tchoi-221194152656 at romulan.bio.brandeis.edu> 
tchoi at binah.cc.brandeis.edu (Giltsu Choi) writes: 

>
>I would like know there is any software
>that I can use my study. here's my situation.
>
>I have 2kb upstream of A gene from two related species
>and 2kb upstream of B gene from a species. B gene is
>coordinately regulated with A gene in terms of
>expression pattern. Now I want to do some sequence
>comparisons to extract information such as
>possible sequence elements for the regulation of these genes.
>Is it possible to extract such things?
>If it is, is there any program or any methods I can use?
>If there isn't, is there any scientists whom I can talk?
>
>I'll appreciate your help.
>
>Sincerely,
>Giltsu Choi
>

There are several ways in which you can perform such an analysis.
While there are several different email servers which will 
search for possible regulatory regions in a queried sequence, 
you may find it easier (and more applicable to the situation 
that you detailed), to first analyze your sequences for regions 
of similarity.  There are several software programs that will search for 
similarities in different sequences, depending upon the type of platform 
you're utilizing (i.e. Unix / DOS / etc.).  Upon determining these 
regions(s) in your sequences, you can utilize a "consensus" sequence as 
a query for the previously mentioned email server search.

Feel free to contact me if you have any further questions:

E-mail: shayashi at mercury.sfsu.edu
        shayashi at ix.netcom.com

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Shigenari Hayashi

E-mail: shayashi at ix.netcom.com
        shayashi at mercury.sfsu.edu