AL2CO ( http://www.ncbi.nlm.nih.gov/pubmed/11524371 ) may be what you need.
It takes the multiple alignment (made by user, so it isn't a black box)
that must contain the sequence of your structure, and maps the positional
conservation in the B-factor column of the structure. To see whether this
is what you want, try:
http://rnajournal.cshlp.org/content/10/11/1698/F1.expansion.html
Although the image was created by Bobscript, this also works fine with Pymol.
Hope this helps,
Mensur
At 02:25 PM 1/29/2009, Anastassis Perrakis wrote:
Dear all,
I was wondering what is the state of the art for this old dark art ...
are there any good servers / programs that allow to easily upload your
own sequence alignments or create a 'transparent' alignment (I want to
see the alignment first and not a total black box) and then allow you
to write out sequence conservation based either on identity or in e.g
a Dayhoff matrix on the B factor column for displaying it later in eg
Pymol?
To be clear I do not want a structural alignment, but mapping sequence
alignment of eg a family to a single structure of a family member.
Thanks in advance, Tassos
==========================================================================
| Mensur Dlakic, PhD | Tel: (406) 994-6576 |
| Department of Microbiology | Fax: (406) 994-4926 |
| Montana State University | Lab: (406) 994-6237 |
| 109 Lewis Hall, P.O. Box 173520 | http://myprofile.cos.com/mensur |
| Bozeman, MT 59717-3520 | E-mail: [email protected] |
==========================================================================
