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M A Roĭtberg

Publications and source records attributed to M A Roĭtberg.

5 recordsLinked to original sources
PubMedDate not supplied

[Pareto-optimal alignment of biological sequences].

The problem of alignment of two symbol sequences is considered. The validity of the available algorithms for constructing optimal alignment depends on the weighting coefficients which are frequently difficult to choose. A new approach to the problem is proposed, which is based on the use of vector weighting functions (instead of tradionally used scalar ones) and Pareto-optimal alignment (an alignment that is optimal at any choice of weighting coefficient will always be Pareto-optimal). An efficient algorithm for constructing all Pareto-optimal alignments of two sequences is proposed. An approach to choosing a "biologically correct" alignment among all Pareto-optimal alignments is suggested.

Algorithms↗
PubMedDate not supplied

[Comparative analysis of primary structure of nucleic acids and proteins].

The review considers the original works on the primary structure of biopolymers, which were carried out from 1983 to 2003. Most works were supported by the Russian program Human Genome and earlier similar Russian programs. Little-known publications of 1983-1993 and recent unpublished results are described in detail. In the field of genome comparisons, these concern the OWEN hierarchic algorithm aligning syntenic regions of two genome sequences. The resulting global alignment is obtained as an ordered chain of local similarities. Alignment of sequences sized about 10(6) nucleotides takes several minutes. The concept of local similarity conflicts is generalized to multiple comparisons. New algorithms aligning protein sequences are described and compared with the Smith-Waterman algorithm, which is now most accurate. The ANCHOR hierarchic algorithm generates alignments of much the same accuracy and is twice as rapid as the Smith-Waterman one. The STRSWer algorithm takes an account of the secondary structures of proteins under study. With the secondary structures predicted using the PSI-PRED software for pairs of proteins having 10-30% similarity, the average accuracy of alignments generated by STRSWer is 15% higher than that achieved with the Smith-Waterman algorithm.

Algorithms↗
PubMedDate not supplied

[The computer program package "SAMSON" for analysis of primary structure of biopolymers].

A program package "SAMSON" for the computer analysis of biopolymer primary structures is described. All possible modes of sequence investigation are considered. The programs for sequence comparison are described in some details. The general principles of a program package organisation and of its user interface are also mentioned. For more complete information see Vernoslov S.E. et al. "Program package "SAMSON" for the analysis of the polymer primary structures", parts 1 and 2, Poustchino, ONTI NCBI, 1989.

Base Sequence↗
PubMedDate not supplied

[Distribution in the genomes of microorganisms of fragments homologous to cDNA of chicken pro-alpha1(1) collagen].

Southern-analysis of genomic DNAs from 14 yeast species (Ascomycetes and Basidiomycetes) with alpha 1(1) chicken collagen cDNA coding for triple-helical domain as a probe, has shown that presence of genomic fragment, homologous to collagen genes of higher eucaryotes, is characteristic for yeasts. In bacterial genomes such fragments are revealed quite rarely. No collagen-like sequences has been found in known yeast proteins by computer-analysis.

Animals↗