Interpreting ConSurf Results: Difference between revisions
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==Average Pairwise Distance== | ==Average Pairwise Distance== | ||
The ''average pairwise distance'' (APD) in a multiple sequence alignment (MSA) is a measure of the evolutionary breadth of the range of sequences included. The APD is "The average number of replacements between any two sequences in the alignment; A distance of 0.01 means that on average, the expected replacement for every 100 positions is 1." (quoted from the ConSurf Server). | The ''average pairwise distance'' (APD) in a multiple sequence alignment (MSA) is a measure of the evolutionary breadth of the range of sequences included. The APD is "The average number of replacements between any two sequences in the alignment; A distance of 0.01 means that on average, the expected replacement for every 100 positions is 1." (quoted from the ConSurf Server). | ||
Generally, an APD of ≲1 is consistent with an MSA whose sequences are limited to proteins with one specific function. As the APD climbs above 1, it is more likely that proteins of multiple functions are included in the MSA. | |||
===Example=== | |||
At the ConSurf Server, click on ''Gallery'', then ''MHC Class I heavy chain'' (2VAA). In the finished results for chain A of 2VAA, under the subheading ''Sequence Data'', click on '''Sequences Used'''. | |||
The APD is 0.99. The MSA has 150 sequences, largely limited to sequences for major histocompatibility complex class I proteins. There is only one class II protein sequence. Three sequences are labeled "zinc-alpha-2-glycoprotein", clearly a different function. There are 22 sequences labeled "uncharacterized protein" which nevertheless have high similarity to the query. 19 sequences are labeled "UPI000... related cluster". | |||