RECON: a program for prediction of nucleosome formation potential

被引:35
作者
Levitsky, VG
机构
[1] Novosibirsk State Univ, Novosibirsk 630090, Russia
[2] Russian Acad Sci, Inst Cytol & Genet, Lab Theoret Genet, Novosibirsk 630090, Russia
基金
俄罗斯基础研究基金会;
关键词
D O I
10.1093/nar/gkh482
中图分类号
Q5 [生物化学]; Q7 [分子生物学];
学科分类号
071010 ; 081704 ;
摘要
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/.
引用
收藏
页码:W346 / W349
页数:4
相关论文
共 17 条
[1]   TGGA repeats impair nucleosome formation [J].
Cao, H ;
Widlund, HR ;
Simonsson, T ;
Kubista, M .
JOURNAL OF MOLECULAR BIOLOGY, 1998, 281 (02) :253-260
[2]   Protective nucleosome centering at splice sites as suggested by sequence-directed mapping of the nucleosomes [J].
Denisov, DA ;
Shpigelman, ES ;
Trifonov, EN .
GENE, 1997, 205 (1-2) :145-149
[3]   NUCLEOSOME POSITIONING BY HUMAN ALU ELEMENTS IN CHROMATIN [J].
ENGLANDER, EW ;
HOWARD, BH .
JOURNAL OF BIOLOGICAL CHEMISTRY, 1995, 270 (17) :10091-10096
[4]   Changes in chromatin accessibility across the GM-CSF promoter upon T cell activation are dependent on nuclear factor κB proteins [J].
Holloway, AF ;
Rao, S ;
Chen, XX ;
Shannon, MF .
JOURNAL OF EXPERIMENTAL MEDICINE, 2003, 197 (04) :413-423
[5]  
IOSHIKHES I, 1993, NUCLEIC ACIDS RES, V21, P4857
[6]   COMPARISONS OF EUKARYOTIC GENOMIC SEQUENCES [J].
KARLIN, S ;
LADUNGA, I .
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 1994, 91 (26) :12832-12836
[7]   What positions nucleosomes? - A model [J].
Kiyama, R ;
Trifonov, EN .
FEBS LETTERS, 2002, 523 (1-3) :7-11
[8]   Twenty-five years of the nucleosome, fundamental particle of the eukaryote chromosome [J].
Kornberg, RD ;
Lorch, YL .
CELL, 1999, 98 (03) :285-294
[9]   Notl flanking sequences:: a tool for gene discovery and verification of the human genome [J].
Kutsenko, AS ;
Gizatullin, RZ ;
Al-Amin, AN ;
Wang, FL ;
Kvasha, SM ;
Podowski, RM ;
Matushkin, YG ;
Gyanchandani, A ;
Muravenko, OV ;
Levitsky, VG ;
Kolchanov, KA ;
Protopopov, AI ;
Kashuba, VI ;
Kisselev, LL ;
Wasserman, W ;
Wahlestedt, C ;
Zabarovsky, ER .
NUCLEIC ACIDS RESEARCH, 2002, 30 (14) :3163-3170
[10]  
Levitsky VG, 2004, BIOINFORMATICS OF GENOME REGULATION AND STRUCTURE, P3