Literature DB >> 15215408

RECON: a program for prediction of nucleosome formation potential.

Victor G Levitsky1.   

Abstract

The program RECON has been designed for constructing profiles of nucleosome potential, characterizing the probability of nucleosome formation along DNA sequences. The program used for recognition of nucleosome formation sites in genomic DNA sequences. It was developed using discriminant analysis based on a genetic algorithm method utilizing statistics for dinucleotide location within local regions of nucleosome formation sites. The program RECON is available at http://wwwmgs.bionet.nsc.ru/mgs/programs/recon/.

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Year:  2004        PMID： 15215408      PMCID： PMC441620          DOI： 10.1093/nar/gkh482

Source DB:  PubMed          Journal:  Nucleic Acids Res        ISSN： 0305-1048            Impact factor:   16.971


  15 in total

Review 1.  Twenty-five years of the nucleosome, fundamental particle of the eukaryote chromosome.

Authors:  R D Kornberg; Y Lorch
Journal:  Cell       Date:  1999-08-06       Impact factor: 41.582

2.  [Locus-controlling regions: description in the LCR-TRRD data base].

Authors:  O A Podkolodnaia; V G Levitskiĭ; N L Podkolodnyĭ
Journal:  Mol Biol (Mosk)       Date:  2001 Nov-Dec

3.  Nucleosome formation potential of eukaryotic DNA: calculation and promoters analysis.

Authors:  V G Levitsky; O A Podkolodnaya; N A Kolchanov; N L Podkolodny
Journal:  Bioinformatics       Date:  2001-11       Impact factor: 6.937

4.  NotI flanking sequences: a tool for gene discovery and verification of the human genome.

Authors:  Alexey S Kutsenko; Rinat Z Gizatullin; Ali N Al-Amin; Fuli Wang; Sergei M Kvasha; Raf M Podowski; Yuri G Matushkin; Anita Gyanchandani; Olga V Muravenko; Viktor G Levitsky; Nikolay A Kolchanov; Alexei I Protopopov; Vladimir I Kashuba; Lev L Kisselev; Wyeth Wasserman; Claes Wahlestedt; Eugene R Zabarovsky
Journal:  Nucleic Acids Res       Date:  2002-07-15       Impact factor: 16.971

Review 5.  What positions nucleosomes?--A model.

Authors:  Ryoiti Kiyama; Edward N Trifonov
Journal:  FEBS Lett       Date:  2002-07-17       Impact factor: 4.124

6.  Identification and characterization of genomic nucleosome-positioning sequences.

Authors:  H R Widlund; H Cao; S Simonsson; E Magnusson; T Simonsson; P E Nielsen; J D Kahn; D M Crothers; M Kubista
Journal:  J Mol Biol       Date:  1997-04-11       Impact factor: 5.469

7.  Nucleosome positioning by human Alu elements in chromatin.

Authors:  E W Englander; B H Howard
Journal:  J Biol Chem       Date:  1995-04-28       Impact factor: 5.157

8.  Nucleosomal DNA sequence database.

Authors:  I Ioshikhes; E N Trifonov
Journal:  Nucleic Acids Res       Date:  1993-10-25       Impact factor: 16.971

9.  Comparisons of eukaryotic genomic sequences.

Authors:  S Karlin; I Ladunga
Journal:  Proc Natl Acad Sci U S A       Date:  1994-12-20       Impact factor: 11.205

10.  Changes in chromatin accessibility across the GM-CSF promoter upon T cell activation are dependent on nuclear factor kappaB proteins.

Authors:  Adele F Holloway; Sudha Rao; Xinxin Chen; M Frances Shannon
Journal:  J Exp Med       Date:  2003-02-17       Impact factor: 14.307
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  18 in total

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Authors:  C Lavelle; A Benecke
Journal:  Eur Phys J E Soft Matter       Date:  2006-02-22       Impact factor: 1.890

2.  "Genome design" model: evidence from conserved intronic sequence in human-mouse comparison.

Authors:  Alexander E Vinogradov
Journal:  Genome Res       Date:  2006-02-03       Impact factor: 9.043

3.  Genome size and metabolic intensity in tetrapods: a tale of two lines.

Authors:  Alexander E Vinogradov; Olga V Anatskaya
Journal:  Proc Biol Sci       Date:  2006-01-07       Impact factor: 5.349

4.  DNA sequence-directed organization of chromatin: structure-based computational analysis of nucleosome-binding sequences.

Authors:  Sreekala Balasubramanian; Fei Xu; Wilma K Olson
Journal:  Biophys J       Date:  2009-03-18       Impact factor: 4.033

5.  Histone modifications, but not nucleosomal positioning, correlate with major histocompatibility complex class I promoter activity in different tissues in vivo.

Authors:  Aparna S Kotekar; Jocelyn D Weissman; Anne Gegonne; Helit Cohen; Dinah S Singer
Journal:  Mol Cell Biol       Date:  2008-09-22       Impact factor: 4.272

6.  Immunity related genes in dipterans share common enrichment of AT-rich motifs in their 5' regulatory regions that are potentially involved in nucleosome formation.

Authors:  Jesus Hernandez-Romano; Francisco J Carlos-Rivera; Heladia Salgado; Hector Lamadrid-Figueroa; Veronica Valverde-Garduño; Mario H Rodriguez; Jesus Martinez-Barnetche
Journal:  BMC Genomics       Date:  2008-07-09       Impact factor: 3.969

7.  A high-resolution map of nucleosome positioning on a fission yeast centromere.

Authors:  Jun S Song; Xingkun Liu; X Shirley Liu; Xiangwei He
Journal:  Genome Res       Date:  2008-04-14       Impact factor: 9.043

8.  Contribution of histone sequence preferences to nucleosome organization: proposed definitions and methodology.

Authors:  Noam Kaplan; Timothy R Hughes; Jason D Lieb; Jonathan Widom; Eran Segal
Journal:  Genome Biol       Date:  2010-11-30       Impact factor: 13.583

9.  The draft genome of the carcinogenic human liver fluke Clonorchis sinensis.

Authors:  Xiaoyun Wang; Wenjun Chen; Yan Huang; Jiufeng Sun; Jingtao Men; Hailiang Liu; Fang Luo; Lei Guo; Xiaoli Lv; Chuanhuan Deng; Chenhui Zhou; Yongxiu Fan; Xuerong Li; Lisi Huang; Yue Hu; Chi Liang; Xuchu Hu; Jin Xu; Xinbing Yu
Journal:  Genome Biol       Date:  2011-10-24       Impact factor: 13.583

10.  RepPop: a database for repetitive elements in Populus trichocarpa.

Authors:  Fengfeng Zhou; Ying Xu
Journal:  BMC Genomics       Date:  2009-01-09       Impact factor: 3.969
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