ReDB: A meiotic homologous recombination rate database

Meiotic recombination occurs preferentially at certain regions in the genome referred to as hot spots which are important for generating genetic diversity and proper segregation of chromosomes during meiosis. Although observations concerning individual hotspots have given clues as to the mechanism of recombination initiation, the nature and causes of recombination rate variation in the genome are still little known. A rational solution is to estimate and rank recombination rates along the genome. Therefore, it is a high demand for a database that deposits and integrates those data to provide a systematical repository of genome-wide recombination rates. Homologous recombination hotspots database is a web-based database of meiotic recombination rates, which comprises enormous data and information of human, mouse, rat, D. melanogaster, C. elegans and yeast. Users can query the database in several alternative ways. The database stores various details for every sequence, such as chromosome number, hyperlinks to the respective reference, and the sequence in FASTA format.

[1]  T. Petes,et al.  Meiotic recombination hot spots and cold spots , 2001, Nature Reviews Genetics.

[2]  P. Donnelly,et al.  A Fine-Scale Map of Recombination Rates and Hotspots Across the Human Genome , 2005, Science.

[3]  J C Murray,et al.  Pediatrics and , 1998 .

[4]  C. Aquadro.  Insights into the evolutionary process from patterns of DNA sequence variability. , 1997, Current opinion in genetics & development.

[5]  R G Steen,et al.  A high-density integrated genetic linkage and radiation hybrid map of the laboratory rat. , 1999, Genome research.

[6]  Zuhong Lu,et al.  Capturing Cryptosporidium. , 1996, Nucleic Acids Res..

[7]  P. Brown,et al.  Global mapping of meiotic recombination hotspots and coldspots in the yeast Saccharomyces cerevisiae. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[8]  T. Matise,et al.  Linkage disequilibrium and inference of ancestral recombination in 538 single-nucleotide polymorphism clusters across the human genome. , 2003, American journal of human genetics.

[9]  K. T. Nishant,et al.  HUMHOT: a database of human meiotic recombination hot spots , 2006, Nucleic Acids Res..

[10]  J. Szostak,et al.  Double-strand breaks at an initiation site for meiotic gene conversion , 1989, Nature.

[11]  P. van Endert,et al.  Genomic polymorphism, recombination, and linkage disequilibrium in human major histocompatibility complex-encoded antigen-processing genes. , 1992, Proceedings of the National Academy of Sciences of the United States of America.

[12]  A. Jeffreys,et al.  Recombination hotspots rather than population history dominate linkage disequilibrium in the MHC class II region. , 2003, Human molecular genetics.

[13]  M. Stephens,et al.  Modeling linkage disequilibrium and identifying recombination hotspots using single-nucleotide polymorphism data. , 2003, Genetics.

[14]  A. Clark,et al.  Local rates of recombination are positively correlated with GC content in the human genome. , 2001, Molecular biology and evolution.

[15]  Liang Chen,et al.  Negative correlation between compositional symmetries and local recombination rates , 2005, Bioinform..

[16]  W. Klitz,et al.  Polymorphism, recombination, and linkage disequilibrium within the HLA class II region. , 1992, Journal of immunology.

[17]  Norman Arnheim,et al.  Hot and cold spots of recombination in the human genome: the reason we should find them and how this can be achieved. , 2003, American journal of human genetics.

[18]  Eric S. Lander,et al.  A comprehensive genetic map of the mouse genome , 1996, Nature.

[19]  D. Gudbjartsson,et al.  A high-resolution recombination map of the human genome , 2002, Nature Genetics.

[20]  A. Jeffreys,et al.  Meiotic recombination hot spots and human DNA diversity. , 2004, Philosophical transactions of the Royal Society of London. Series B, Biological sciences.

[21]  David Haussler,et al.  Comparative recombination rates in the rat, mouse, and human genomes. , 2004, Genome research.

[22]  Eric S. Lander,et al.  Human genome sequence variation and the influence of gene history, mutation and recombination , 2002, Nature Genetics.

[23]  S. Keeney,et al.  Where the crossovers are: recombination distributions in mammals , 2004, Nature Reviews Genetics.

[24]  P. Donnelly,et al.  The Fine-Scale Structure of Recombination Rate Variation in the Human Genome , 2004, Science.

[25]  Xiao Sun,et al.  Support vector machine for classification of meiotic recombination hotspots and coldspots in Saccharomyces cerevisiae based on codon composition , 2005, BMC Bioinformatics.

[26]  L. Duret,et al.  Does recombination improve selection on codon usage? Lessons from nematode and fly complete genomes , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[27]  A. Goldman,et al.  Meiotic recombination hotspots. , 1995, Annual review of genetics.

[28]  J. Wall,et al.  Linkage disequilibrium patterns across a recombination gradient in African Drosophila melanogaster. , 2003, Genetics.