Multiple sequence alignment based on new approaches of tree construction and sequence comparison
- Russian Academy of Sciences, Novosibirsk (Russian Federation). Inst. of Cytology and Genetics
- National Research Council, Milan (Italy). Inst. of Biomedical Advanced Technology
A fast algorithm for multiple sequence alignment based on new approaches of tree construction and sequence comparison is suggested. The authors developed a version of the pairwise sequence alignment algorithm,` which was based on analysis of DOT matrix Diagonal fragments (Df) followed by joining of significant Dfs in the final alignment. The algorithm maintains some methodological features of Needleman-Wunsch (NW) type algorithms and uses statistical estimations of similarity of various Dfs. The estimations were entered into a compact ``competition matrix`` (CM). Homology of sequence positions for multiple alignment was changed to homology of the corresponding rows in the aligned subsets. In addition, instead of one-iteration filling of the CM by Df information, a multi-iteration method was suggested. The authors assumed that the minimal length of Df used for each iteration must be selected so that the probability of occurrence of homologous subsequences of a given length, by chance, would be low. On the basis of these significant Dfs they reconstructed an initial rough alignment. The method of multiple alignment presented here also uses a new approach for tree reconstruction based on the analysis of the relatively conserved oligonucleotides in a given set. This approach has some advantages compared to traditional methods of phylogenetic tree reconstructions. The method was tested on 5S RNA sequences and its application for contigs joining was discussed.
- OSTI ID:
- 37550
- Report Number(s):
- CONF-9206273-; ISBN 981-02-1157-0; TRN: IM9519%%475
- Resource Relation:
- Conference: 2. international conference on bioinformatics, supercomputing, and complex genome analysis, St. Petersburg, FL (United States), 4-7 Jun 1992; Other Information: PBD: 1993; Related Information: Is Part Of The second international conference on bioinformatics, supercomputing and complex genome analysis; Lim, H.A. [ed.] [Florida State Univ., Tallahassee, FL (United States). Supercomputer Computations Research Inst.]; Fickett, J.W. [ed.] [Los Alamos National Lab., Los Alamos, NM (United States). Center for Human Genome Studies]; Cantor, C.R. [ed.] [Boston Univ., MA (United States). Center for Advanced Research in Biotechnology]; Robbins, R.J. [ed.] [Johns Hopkins Univ., Baltimore, MD (United States). Applied Research Lab.]; PB: 672 p.
- Country of Publication:
- United States
- Language:
- English
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