Abstract:
BACKGROUND:Conservation and variation scores are used when evaluating sites in a multiple sequence alignment, in order to identify residues critical for structure or function. A variety of scores are available today but it is not clear how different scores relate to each other. RESULTS:We applied 25 conservation and variation scores to alignments from the Catalytic Site Atlas (CSA). We calculated distances among scores based on correlation coefficients, and constructed a dendrogram of the scores by average linking cluster analysis. The cluster analysis showed that most scores fall into one of two groups--substitution matrix based group and frequency based group respectively. We also evaluated the scores' performance in predicting catalytic sites and found that frequency based scores generally perform best. CONCLUSIONS:Conservation and variation scores can be classified into mainly two large groups. When using a score to predict catalytic sites, frequency based scores that also consider a background distribution are most successful.
journal_name
BMC Bioinformaticsjournal_title
BMC bioinformaticsauthors
Johansson F,Toh Hdoi
10.1186/1471-2105-11-388subject
Has Abstractpub_date
2010-07-21 00:00:00pages
388issn
1471-2105pii
1471-2105-11-388journal_volume
11pub_type
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