Calcium-Binding Protein Protocols Calcium-Binding Protein Protocols

Multiple Sequence Alignment 249
program (47), which constructs multiple alignments based on segment-to-segment
comparisons rather than the residue-to-residue comparisons used previously.
The segments are incorporated into a multiple alignment using an
iterative procedure. The PRRP program (46) optimizes a progressive, global
alignment by iteratively dividing the sequences into two groups which are
subsequently realigned using a global group-to-group alignment algorithm.
PRALINE (14) employs profile-preprocessing and secondary structure prediction
to guide the alignments in an optionally iterative fashion.
The program SAGA (71) does not employ DP, but uses a genetic algorithm
(GA) to select from an evolving alignment population the alignment, which
optimizes, as an Objective Function (OF), the weighted sum of pairs as used in
the MSA program (66). More recently, a measure of consistency between the
considered multiple alignment and a corresponding library of CLUSTAL
pairwise alignments was taken. This OF was developed for the COFFEE algorithm
(43). As mentioned in Subheading 4.1., Hidden Markov models (HMM)
have also been attempted as statistical models of the primary structure consensus
for a sequence family (41,42). The program HMMT (48) uses a simulatedannealing
method to maximise the probability that an HMM represents the
sequences to be aligned.
References
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Structural and functional diversity, Protein Sci. 5, 2375–2390.
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Brownlee, G. G. (1991) Key residues involved in calcium-binding motifs in
EGF-like domains. Nature 351, 164–167.
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Protein Profiles 2, 305–490.
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8. Nakayama, S., Moncrief, N. D., and Kretsinger, R. H. (1992) Evolution of
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diverse evolutionary histories. J. Mol. Evol. 34, 416–448.
9. Kretsinger, R. H. and Nakayama, S. (1993) Evolution of EF-hand calcium-modulated
proteins. IV. Exon shuffling did not determine the domain compositions of
EF-hand proteins. J. Mol. Evol. 36, 477–488.