Additional file 4.

CDK-SCTTLRE subfamily CHAIN alignment versus the CDK family. Colorized sequence alignment and partition generated by the CHAIN program, comparing the apicomplexan-specific subfamily of CDKs to a diverse set of eukaryotic CDKs. CHAIN compares a given "query" set (here, members of the putative subfamily) to a larger "main" set (here, a diverse set of eukaryotic CDKs) and divides the main set into 3 partitions based on contrasting levels of residue conservation: a "foreground" set of sequences with residue motifs matching the query, a "background" which does not conserve the distinguishing motifs of the foreground, and an "intermediate" which contains sequences that may partially match both the foreground and background sequence motifs. The alignment summary generated by CHAIN displays only the aligned sequences in the query, but highlights the alignment columns according to the conservation patterns defining each partition. The alignment appears as three blocks, labeled "Intermediate", "Background" and "Foreground", corresponding to those partitions. Above each block is a histogram indicating residue conservation patterns unique to that sequence set; dots above each column indicate which columns form the distinguishing pattern. Thus, tall red bars above columns in the "Foreground" block indicate residues that are strikingly conserved in the foreground, but not in the background. The rows below each "Background" and "Foreground" block indicate the conserved residue types and their conservation levels within those sequence sets, in units of 10%.

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Talevich et al. BMC Evolutionary Biology 2011 11:321   doi:10.1186/1471-2148-11-321