Sandbox2 Eric Martz: Difference between revisions
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Here are the distributions of conservation grades for 2VAA:A using different total numbers of sequences in the multiple sequence alignment (from the jobs linked in the above table). | Here are the distributions of conservation grades for 2VAA:A using different total numbers of sequences in the multiple sequence alignment (from the jobs linked in the above table). | ||
[[Image:Consurf 2vaa distributions.gif|center]] | |||
<center> | |||
[http://spreadsheets.google.com/ccc?key=pOkZ8Eknd7bVJqZpSfiejAA This graph] was prepared with | |||
[http://spreadsheets.google.com Google Spreadsheets]. | |||
</center> | |||
I was '''not surprised''' to see: | |||
# The number of residues with conservation level-9 go down dramatically with increased number of sequences and increased APD<ref name="apd">APD: Average Pairwise Distance, a measure of the sequence diversity in the multiple sequence alignment.</ref>. | |||
# A compensating rise in the number of residues with intermediate conservation levels, notably levels 4-6. | |||
I was '''surprised''' to see: | |||
<ol start="3"> | |||
<li> The number of sequences and APD<ref name="apd" /> have very little effect on the numbers of residues in conservation levels 1-3 (gray zone) and a minor effect on levels 7-8 (light gray zone). The constancy of level 1 was particularly surprising. | |||
</li> | |||
<li> Almost no difference between the distributions for 218 sequences in ConSurf vs. 144 in ConSurf-DB, surprising given that the APDs<ref name="apd" /> were 1.17 and 1.72 respectively. | |||
</li> | |||
</ol> | |||
Of course some of these observations may not generalize to other protein chains. It would be useful to analyze more cases. | |||
==References== | ==References== | ||
<references /> | <references /> | ||