CYRCA is a program for multiple alignment of protein profiles. Its input are pairwise alignments of blocks found by the LAMA program. CYRCA first identifies consistent transitive alignments between groups of three blocks (triangular sets). Triangular sets with common alignments are next joined together to form larger sets. Finally any linear edges with very high sores are added to the sets. More information on CYRCA, LAMA and their uses can be found at NAR 24:3836 '96 (LAMA) MGG 254:689 '97 (LAMA usage) PNAS USA 94:8421 '97 (LAMA usage) JMB 307:939 '01 (CYRCA) TIBS 28:473 '03 (CYRCA usage) LAMA can be used and is also described at the Blocks WWW site.
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