By V. G. Levitsky, A. V. Katokhin, O. A. Podkolodnaya, D. P. Furman (auth.), Nikolay Kolchanov, Ralf Hofestaedt (eds.)
Bioinformatics of Genome legislation and Structurecovers:
-regulatory genomic sequences: databases, wisdom bases, laptop research, modeling, and popularity;
-large-scale genome research and useful annotation;
-gene constitution detection and prediction;
-comparative and evolutionary genomics;
-computer research of genome polymorphism and evolution; computing device research and modeling of transcription, splicing, and translation; structural computational biology: structure-function association of genomic DNA, RNA, and proteins;
-gene networks, sign transduction pathways, and genetically managed metabolic pathways: rules of association, operation, and evolution;
-data warehousing, wisdom discovery and knowledge mining; and,
-analysis of simple styles of genome operation, association, and evolution.
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Extra info for Bioinformatics of Genome Regulation and Structure
Presence of tRNA-like sequences was detected in various genetic structures. Their relative distribution pattern over these sequences and preliminary functiQnal analysis are presented. Key words: tRNA-like sequence, interspersed repeats, functional analysis, computer analysis 1. INTRODUCTION The goal of the work was to detect evolutionary ancestors and relatives of known tRNAs. In contrast to the majority of available tRNA search algorithms (like tRNA-Scan SE; Lowe, 1997) that are developed to detect functional tRNA genes by using information on their secondary structure and other tRNA-specific features, the method developed is intended only for showing up evolutionary relationships.
M. S. l. G. 4* 1Institute of Cytology & Genetics, Siberian Branch of the Russian Academy of Sciences, prosp. ru; 2 Ugra Research Institute of Information Technologies, ul. Mira ISI, Khanty-Mansyisk, 6280I I Russia; 3National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bldg. 38A, Bethesda, MD 20894, USA; 4Novosibirsk State University, ul. Pirogova 2, Novosibirsk, 630090 Russia Corresponding author * Abstract A new method for the recognition of type 2 promoters in the eukaryotic tRNA genes, which takes into consideration not only nucleotide distribution at individual box positions, but also the multiple interactions between the different parts of the A and B boxes, is proposed.
The most frequent mechanism of indel formation is one that involves inverted repeats in both the deletion and the insertion event with the deletion occurring first (14 times). Mechanisms involved Moebius loop resolution and breakage or excision mediated by 20 Computational Genomics symmetric elements via paths "deletion frrst, insertion second" and "insertion occurs frrst, 5 to the fragment to be deleted" were assigned to 12 and 11 indels respectively. For example, reported indel delGTinsCC in the CTNS gene (CX994477) was found to be mediated by symmetric elements via path "insertion occurs frrst, 5 1 to the fragment to be deleted".
Bioinformatics of Genome Regulation and Structure by V. G. Levitsky, A. V. Katokhin, O. A. Podkolodnaya, D. P. Furman (auth.), Nikolay Kolchanov, Ralf Hofestaedt (eds.)