Paul Davis writes:
>... is working on the mammalian D-loop of mitochondrial DNA and is looking
>for a program that finds optimal sequence alignment and assigns gaps.
>It would be good if the software also does multiple alignments of both
>closely and distantly related species.
>If anyone out there has any suggestions, please email me at
>karyn at connect.com.au
>I will post a summary.
>karyn at connect.com.au
We use CLUSTALV which is distributed as C source code and which can be installed on DOS, Mac, Unix and VMS systems. You can get the package by anonymous ftp at the Indiana, Houston, and EMBL molecular biology distribution sites. Their network addresses are respectively:
ftp.bio.indiana.edu
ftp.bchs.uh.edu
ftp.embl-heidelberg.de
In the Indiana archive one must enter directory molbio/align. In the Houston
archive it is in directory pub/gene-server in all of the four sub directories dos, Mac, unix, and vms. On the EMBL archive it is in pub/software/unix or
pub/software/vax.
You can play with the aligment parameters of CLUSTALV to get what you want. You would need to align the closely related seqs first using one set of parameters and then do a profile alignment (which does not alter the alignment already made) with the more distantly related seqs using different parameters.
Another package which you will find very useful is called GDE. It allows (among many other things) the user to edit computer aligned seqs by hand. You will find this 'tidying up' to be essential. The GDE system runs under Unix and employs Xwindows. The latest version is GDE2.2a and it is available by anonymous ftp from megasun.bch.umontreal.ca or golgi.harvard.edu
