DETECTING SUBTLE SEQUENCE SIGNALS - A GIBBS SAMPLING STRATEGY FOR MULTIPLE ALIGNMENT

Citation
Ce. Lawrence et al., DETECTING SUBTLE SEQUENCE SIGNALS - A GIBBS SAMPLING STRATEGY FOR MULTIPLE ALIGNMENT, Science, 262(5131), 1993, pp. 208-214
Citations number
116
Categorie Soggetti
Multidisciplinary Sciences
Journal title
ISSN journal
00368075
Volume
262
Issue
5131
Year of publication
1993
Pages
208 - 214
Database
ISI
SICI code
0036-8075(1993)262:5131<208:DSSS-A>2.0.ZU;2-O
Abstract
A wealth of protein and DNA sequence data is being generated by genome projects and other sequencing efforts. A crucial barrier to decipheri ng these sequences and understanding the relations among them is the d ifficulty of detecting subtle local residue patterns common to multipl e sequences. Such patterns frequently reflect similar molecular struct ures and biological properties. A mathematical definition of this ''lo cal multiple alignment'' problem suitable for full computer automation has been used to develop a new and sensitive algorithm, based on the statistical method of iterative sampling. This algorithm finds an opti mized local alignment model for N sequences in N-linear time, requirin g only seconds on current workstations, and allows the simultaneous de tection and optimization of multiple patterns and pattern repeats. The method is illustrated as applied to helix-turn-helix proteins, lipoca lins, and prenyltransferases.