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", "Back