By V. G. Levitsky, A. V. Katokhin, O. A. Podkolodnaya, D. P. Furman (auth.), Nikolay Kolchanov, Ralf Hofestaedt (eds.)
Bioinformatics of Genome law and Structurecovers:
-regulatory genomic sequences: databases, wisdom bases, machine 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; desktop 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 uncomplicated styles of genome operation, association, and evolution.
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Extra info for Bioinformatics of Genome Regulation and Structure
A lot of tRNA-like sequences in D-loop regions of vertebrates show that displacement loop in mitochondrial DNA has evident similarity to tRNA. A displacement loop region contains a site of mitochondrial heavy chain replication and promoters for transcription of heavy and light chains (Clayton, 1984). Although individual occurrence of structural similarity of a D-loop to tRNA was mentioned earlier, the similarity of D-loop primary sequences to each other and to tRNAs has not been noticed (Mans, 1991).
The repair of this region by DNA polymerase would generate the duplication of a sequence from the end of the symmetric element that was originally disconnected. This may have occurred in the case of a micro-insertion in theABCDJ (CI014470) gene CCACGCCTACc~GCCTCTACT. It appears likely that it was the first C rather than the second that was inserted. Mechanisms based upon either secondary loop excision or quasi-palindrome correction were found to be able to account for -18% of micro-deletions and -15% of micro-insertions.
Layout of construction of insertion regions of LTR retrotransposons. , 1998). 2 Evaluating characteristics of mononucleotide context in insertion regions It is assumed that nucleotide bases occur at each position of insertion regions independently of one another with frequencies calculated according to the Release 2 of D. 215 for C and G. 25 Part 1 In this case, the set of nucleotide frequencies at each position of the 60-symbol sequence follows a multinomial distribution (Agresti, 1996). Sum of the probabilities to obtain the observed or larger deviations of nucleotide frequencies of each type from the expected values (W) according to random causes gives the estimate of context variation at each position of the insertion region sequence sample.