[Verification of the PREFAB alignment database].

The verification of the PREFAB database containing golden standard protein alignments was performed. It has revealed a significant number of differences between the sequences from PREFAB and PDB databases. It was shown that compared to the sequences given in the PDB database 575 alignments refered to a sequence with a gap; such alignments were excluded. Furthermore, compared to the PDB-sequences a single substitute or the insertions were found for 440 aminoacid sequences from PREFAB database; these sequences were edited. SCOP domain analysis has shown that only 502 alignments in the resulting set contain the sequences from the same family. Finally, eliminating duplicates, we have created a new golden standard alignment database PREFAB-P based on PREFAB; the PREFAB-P database contains 581 alignments.

[Increasing the accuracy of the global alignment of amino acid sequences by constructing a set of alignment candidates].

The accuracy of the global Smith-Waterman alignments and Pareto-optimal alignments depending on the degree of sequence similarity (percent of coincidence, % id, and the number of remote fragments NGap) has been examined. An algorithm for constructing a set of three to six alignments has been developed of which the accuracy of the best alignment exceeds on the average the accuracy of the best alignment that can be constructed using the Smith-Waterman algorithm. For weakly homologous sequences (% id 15, NGap 20), the increase in the accuracy is on the average about 8%, with the average accuracy of the global Smith-Waterman alignments being about 38% (the accuracy was estimated on model test sets).

[Computation of the probabilities of families of biological sequences].

An algorithm for computing the probabilities of families of biological sequences is presented. The algorithm is applicable to many problems of bioinformatics, in particular, for computing the sensitivity of seeds while searching for local similarities in genomes and while estimating the reliability of search for clusters of regulatory sites. This algorithm can be also used for distribution of probabilities described by different models, for example, Bernoulli, Markov, and hidden Markov models. The algorithm is based on the description of probabilities distribution as well as on the description of the family of sequences using the finite automaton. Then the problem of calculation of probabilities is reduced to computation of the proper generalized statistical sum. The algorithm can be applied not only to biological sequences but also to symbol sequences of any origin.

[A new approach to estimating the significance of identification of deletion inserts in pairwise alignment].

Within the framework of the unique method of estimating the significance of pairwise alignment of nucleotide sequences, developed by the authors, a new approach to the analysis of deletion inserts in pairwise alignment has been realized. It was shown that the decrease in the average integral length of deletion inserts in alignments obtained using the modern algorithms, as compared with true alignments, is related to a decrease in the number of some deletion inserts rather than a decrease in their average length.

[Statistical analysis of DNA sequences nearby splicing sites].

Recognition of coding regions within eukaryotic genomes is one of oldest but yet not solved problems of bioinformatics. New high-accuracy methods of splicing sites recognition are needed to solve this problem. A question of current interest is to identify specific features of nucleotide sequences nearby splicing sites and recognize sites in sequence context. We performed a statistical analysis of human genes fragment database and revealed some characteristics of nucleotide sequences in splicing sites neighborhood. Frequencies of all nucleotides and dinucleotides in splicing sites environment were computed and nucleotides and dinucleotides with extremely high\low occurrences were identified. Statistical information obtained in this work can be used in further development of the methods of splicing sites annotation and exon-intron structure recognition.

Radiographic assessment of Gardner's syndrome.

The detection of osteomas in the maxillofacial region may be the initial clinical finding in Gardner's syndrome (GS). The most common location of osteomas is in the skull, but the lesion can also occur in the jaws. We present a case of a 47 year old male patient with GS who was referred for radiological evaluation. Extraoral examination revealed an epidermoid cyst and the patient had a history of intestinal polyps. A panoramic radiograph demonstrated numerous osteomas and diffuse sclerosis of the mandible, and compound odontomas with impacted teeth. CT scan allowed the localization and extension of the osteomas, and showed other sites in the maxillofacial region as well. CT images also revealed a different behaviour of osteoma, invading the mandibular canal.

[Comparative analysis of primary structure of nucleic acids and proteins]. / Sravnitel'nyi analiz pervichnykh struktur nukleinovykh kislot i belkov.

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.

[Pareto-optimal alignment of biological sequences]. / Pareto-oppimal'nye vyravnivaniia biologicheskikh posledovatel'nostei.

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.

[Distribution in the genomes of microorganisms of fragments homologous to cDNA of chicken pro-alpha1(1) collagen]. / Rasprostranenie v genomakh mikroorganizmov fragmentov, gomologichnykh kDNK pro-alpha1(1) kollagena tsyplenka.

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.

[The computer program package "SAMSON" for analysis of primary structure of biopolymers]. / Paket programm dlia analiza pervichnykh struktur biopolimerov "SAMSON".

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.