Amino acid conservation

Jalview Discussion
1

Hello all,

Could someone provide me with a clearer understanding as to why the conservation index values go to 9 and are then + or * above this? I presume * is 100% conserved, but what about +?

Thanks in advance,

Brendan.

2

Hello Brendan.

Could someone provide me with a clearer understanding as to why the conservation index values go to 9 and are then + or * above this? I presume * is 100% conserved, but what about +?

OK - I guess by clearer, you mean clearer than this page: http://www.jalview.org/help/html/calculations/conservation.html

The conservation measure counts the number of amino acid properties conserved in a column - when all 10 properties are conserved, the measure would be 10, but then its useful to reflect whether the column contains a conserved residue, or one or more substitutions between residues with the same physicochemical property. Because we wanted a per-column symbol, we use '*' to mean the column is conserved (ie conservation==11), and '+' to means the column contains residues with the same physicochemical properties (conservation == 10).

Hope that clears up any confusion - I'll amend the built in documentation to explicitly mention the */+ convention.
Jim.

···

On 24/05/2012 10:14, Palmer, Brendan wrote:

3

I did look at the documentation but unfortunately I could not access the AMAS paper. It just seemed odd that when I hold my mouse pointer over the individual positions on the graphical output 10 and 11 appear, despite + and * being displayed on the X-axis.

4

The full PDF of the AMAS paper (and our other early papers) is here:

http://www.compbio.dundee.ac.uk/ftp/pdf/Protein_sequence_alignments_a_strategy_for_the_hierarchical_analysis_of_residue_conservation_1993.pdf

Geoff.

···

From: jalview-discuss-bounces@jalview.org [mailto:jalview-discuss-bounces@jalview.org] On Behalf Of Jim Procter
Sent: 24 May 2012 12:04
To: Palmer, Brendan
Cc: Jalview-discuss@jalview.org
Subject: Re: [Jalview-discuss] Amino acid conservation

Hi Brendan.

On 24/05/2012 11:00, Palmer, Brendan wrote:

Thanks for the immediate response.

:slight_smile:

I did look at the documentation but unfortunately I could not access the AMAS paper. It just seemed odd that when I hold my mouse pointer over the individual positions on the graphical output 10 and 11 appear, despite + and * being displayed on the X-axis.

ah - yes - well spotted. I’ve logged this in our bug tracker (http://issues.jalview.org/browse/JAL-1107) and documentation is now fixed in the next release.

If you’re interested, you can see a version of the AMAS paper here:
http://www.compbio.dundee.ac.uk/papers/amas/amas3d.html

Jim.