[Chimera-users] Analysis of the multiple alignments + structures

[Elaine Meng]

HI James,
Sorry, Chimera does not do evolutionary trace calculations.  I would definitely have mentioned it if it did!  In Chimera, if you input a tree along with your alignment, you can click a node on the tree and easily extract only the sequences for that node, but there is nothing to compare the residues from one set of sequences with those from another set of sequences, other than looking at the separate alignment windows yourself.  Also, Chimera cannot create the tree, it must be read in from a file.
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/framemav.html>
… see the section on Trees:
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/multalignviewer.html#trees>
… example image of tree+alignment in Chimera:
<http://www.rbvi.ucsf.edu/chimera/data/tutorials/systems/redoxin/ConSurf-1hd2-chimera19-seq.png>

Although I’m still very interested in GPCRs, I have not actively worked on them for  >10 years, so I’m not the best person to ask for current information.  I know there is a GPCRdb, but I don’t know if it has been kept up to date.  You could try googling or pubmed-searching for “gpcr alignments” or similar terms.

Two ideas for evolutionary trace:

(1) The Lichtarge group has an evolutionary trace server. 
<http://mammoth.bcm.tmc.edu/ETserver.html>

 At first I thought you could only put in a PDB ID and not have any control over what sequences are used (which might not be useful for your research), but then I noticed a “GPCRs” link on the left-hand side.  Click that and it lets you choose specific GPCR subsets, which sounds exactly like the kind of calculation you wanted.  I don’t know if it includes your specific groups of interest, however, and  I don’t see a way to use your own alignments.
<http://mammoth.bcm.tmc.edu/gpcr/diff_GPCRA.html>

(2) JEvTrace, a Java implementation of evolutionary trace.
<http://compbio.berkeley.edu/people/marcin/jevtrace/>

I have one correction to that page. It says you can show results using the MSF Viewer tool in Chimera, which no longer exists.  You can still use Chimera, just the Multalign Viewer tool instead (Multalign Viewer menu: "File… Load SCF/Seqsel File” will open the file from JEvTrace).  I’ll email the author and tell him to update that information.

Those are all my ideas.  If neither helps you, you may have to continue searching for programs or other tools and instructions on how to do the steps of the analysis yourself.
I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Sep 4, 2014, at 11:39 PM, James Starlight <jmsstarlight at gmail.com> wrote:

> Elaine,
> 
> onequestion about your 2003 GPCRs study: in this paper you've used the method called differential evolution tracing to detect functionally-relevant amino acids for rhodopsin only (substration of the conservative residues found in rhodopsin from those found in whole set of A-class GPCRs). I wounder if there any possibility for this method in Chimera's mutalign (in case where I have big alignment with thesequences of all olfactory receptors) to substract residues found in one philogenetic branch (corresponded to specified sub-class or group of those receptors) from the residues common to all olfactory receptors or (ii) substract residues common for the all olfactory receptors from those common to all A-class GPCRs? BTW do you know open-access data-bases consisted of the evolutional (alignments) information to the GPCRs? it's intresting to compare my alignment with some references. 
> 
> Thanks for help,
> 
> James