conservation score on multiple protein alignment

Jalview Discussion
1

Hi,

I’m a first time user of JalView. I performed a multiple sequence alignment on a small set of protein sequences (11) using Clustal W2, and used JalView 2.8.2 to view and format the alignment using JalView’s default parameters. I’m getting ready to publish this figure for a paper, but couldn’t find any documentation for what the numbers (ranging from 0-9) under the conservation histogram mean. Would really appreciate any help I can get.

Thanks.

Bhanu Rajput

2

Hi Bhanu,
I believe the conservation calculations are explained here (well, mainly in the Livingstone and Barton paper that they cite):

http://www.jalview.org/help/html/calculations/conservation.html

Best,
Elaine

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Elaine C. Meng, Ph.D.
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Feb 20, 2015, at 11:42 AM, Rajput, Bhanu (NIH/NLM/NCBI) [E] <rajput@ncbi.nlm.nih.gov> wrote:

Hi,

I’m a first time user of JalView. I performed a multiple sequence alignment on a small set of protein sequences (11) using Clustal W2, and used JalView 2.8.2 to view and format the alignment using JalView’s default parameters. I’m getting ready to publish this figure for a paper, but couldn’t find any documentation for what the numbers (ranging from 0-9) under the conservation histogram mean. Would really appreciate any help I can get.

Thanks.

Bhanu Rajput