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New PDF release: 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.)

ISBN-10: 1441971521

ISBN-13: 9781441971524

ISBN-10: 147574613X

ISBN-13: 9781475746136

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; machine 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: ideas of association, operation, and evolution;
-data warehousing, wisdom discovery and information mining; and,
-analysis of simple styles of genome operation, association, and evolution.

The information provided can be used whereas fixing quite a lot of difficulties, either uncomplicated and utilized, in numerous instructions of molecular biology, molecular genetics, biotechnology, pharmacogenetics, pharmacology, and adjoining fields of medication, veterinary, and agrobiology.

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Additional info for Bioinformatics of Genome Regulation and Structure

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3. RESULTS All data concerning the tRNA-like sequences are presented in Tables 1-3. All the data listed in tables do not contain the known tRNA genes and tRNA-like sequences that were found in tRNA-derived repeats 42 Computational Genomics (like Alu, MIRs, B2, and so on). All these repeats where deleted using RepBase and GenBank annotations. Alu and MIR repeats were also excluded from findings using the method described above (Korotkov, 2000). Table 1. The numbers of tRNA-like sequences detected in earlier characterized DNA regions ofthe GenBank's nine basic taxonomic divisions Feature 3'UTR S'UTR CDS D-loop Enhancer exon gene iONA VRL PHG BCT PLN 1 4 363 14 398 358 Division INV VRT 2 3 2 103 45 ROD 22 6 107 299 MAM 4 2 87 11 PRI 287 78 9312 12 3 2 4 3 133 29 277 11 2 40 5 433 19 296 30 1 1 1512 7851 2 1541 intron 6 64 26 12 311 112 28 LTR 11 11 mat_peptide 2 1 9 misc_feature 153 18 6715 21 11 490 348 29 60 misc_RNA 21 2 8 281 9 5 misc_signal 9 1 mRNA 1 2 27 13 371 6 3 5 5 precursor_RNA 4 47 2 6 5 29 3 prim_transcript 2 289 4 6 4 11 primer_bind 2 1 5 80 4 206 promoter 8 protein_bind 4 17 repeat_region 29995 31 54 12 421 111 8 repeat_unit 29 16 20 104 42 72 rRNA 231 264 70 19 2 6 76 satellite 1 2 8 12 14 1 scRNA sig_peptide 13 4 snRNA stem_loop 2 2 STS 147 V_region 176 V_segment 4 104012 unassigned 65 38 717 1214 2157 462 1900 263 162749 Total 496 66 2225 2758 2921 1054 3450 755 The region definitions in the column "Feature" are presented as the GenBank's standard features.

Thus, local CPCP represent a certain code determining interaction of the integration complex with genomic DNA in the insertion regions. Note that analysis of CPCP in insertion regions gives more information compared with contextual analysis, as it allows for detection of DNA secondary structure characteristics that are essential for interaction with the integration complex. Preferential insertion of the elements into the regions displaying certain local CPCP may reflect the functional distinctions between integration events, in particular, resulting from different structures of DNA-recognizing domains of integrases of various LTR retrotransposons.

6 (data not shown). The second group--insertion regions of the elements gypsy, HMSBeagle, tirant, and yoyo. Distribution of CPCP along the insertion regions for the elements of this group is illustrated by the example of average values of the property No. 27 (tilt) of tirant insertion regions (Figure 4). Melting temperature (No. 22) in 297 insertion region 5 9 13 17 21 25 29 33 37 41 45 49 53 57 Dinucleotide position Figure 3. Profile of melting temperature (property No. 22 in the database PROPERTY) of the dinucleotides over the insertion region of LTR retrotransposon 297.

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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.)

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