[Bioclusters] Multiple Sequence Alignment

Jonathan Barber bioclusters@bioinformatics.org
Mon, 10 Feb 2003 11:08:02 +0000

On Fri, Feb 07, 2003 at 01:43:37PM -0600, Borries Demeler wrote:
> Sorry for this slightly off-topic question:
> I need to support a bioinformatics core facility where a lot of genomics
> is done under Unix. To help with alignment display and editing, I am
> looking for a graphical multiple sequence alignment editor for Unix/X
> capable of the following features:
> * needs to be able to display hundreds of sequences
> * shade by the degree of conservation
> * shade by residue property (hydrophobic, acidic, etc...)
> * various import formats desirable
> * manually edit and save changes capabilities
> What is everyone using for these purposes, recommendations?

Jalview (http://circinus.ebi.ac.uk:6543/jalview/) is a Java application
that does these things, but I've not really used it in anger, so you'll
have to try it and see.

> Thanks a lot, -Borries
> ---
> Borries Demeler, Ph.D.
> Assistant Professor
> The University of Texas Health Science Center at San Antonio
> Dept. of Biochemistry, 7703 Floyd Curl Drive, San Antonio, Texas 78229-3900
> Voice: 210-567-6592, Fax: 210-567-4575, Email: demeler@biochem.uthscsa.edu