Comparative analysis and visualization of multiple collinear genomes

BMC Bioinformatics

Volumn 13, Issue SUPPL.3, 2012, Pages

  Wang, Jeremy R ^a   de Villena, Fernando Pardo Manuel ^b   McMillan, Leonard ^a  

^a CB 3175 Sitterson Hall   (United States)

^b UNIVERSITY OF NORTH CAROLINA SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

COMPARATIVE ANALYSIS; DATA CONTENTS; DYNAMIC VISUALIZATION; GENOME BROWSERS; GENOMIC DATA; GENOMIC DATA SETS; HAPLOTYPES; INTERACTIVE NAVIGATIONS; MODEL ORGANISMS; MULTIPLE DATA SETS; PHYLOGENETIC TREES; VARIABLE RESOLUTION; VISUALIZATION AND ANALYSIS; VISUALIZATION TOOLS; WEB-BASED TOOLS;

BIOLOGY; DATA VISUALIZATION; VISUALIZATION;

GENES;

ANIMAL; ARTICLE; CLASSIFICATION; CLUSTER ANALYSIS; COMPARATIVE STUDY; COMPUTER PROGRAM; GENETICS; GENOME; INTERNET; MOUSE; MOUSE STRAIN; PHYLOGENY; SINGLE NUCLEOTIDE POLYMORPHISM;

ANIMALS; CLUSTER ANALYSIS; GENOME; INTERNET; MICE; MICE, INBRED STRAINS; PHYLOGENY; POLYMORPHISM, SINGLE NUCLEOTIDE; SOFTWARE;

EID: 84867328380     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-13-S3-S13     Document Type: Article

References (17)

1. Krzywinski M, et al. Circos: an information aesthetic for comparative genomics. Genome Res 2009, 19:1639-1645. 10.1101/gr.092759.109, 2752132, 19541911.
2. Brodie R, Roper RL, Upton C. JDotter: a Java interface to multiple dot plots generated by dotter. Bioinformatics 2004, 20(2):279-281. 10.1093/bioinformatics/btg406, 14734323.
3. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol 1990, 215:403-410.
4. Frazer KA, Pachter L, Poliakov A, Rubin EM, Dubchak I. VISTA: computational tools for comparative genomics. Nucleic Acids Res 2004, 32:W273-W279. 10.1093/nar/gkh458, 441596, 15215394.
5. Kent WJ, Sugnet CW, Furey TS, Roskin KM, Pringle TH, Zahler AM, Haussler D. The human genome browser at UCSC. Genome Res 2002, 12:996-1006. 186604, 12045153.
6. Stein LD, Mungall C, Shu S, Caudy M, Mangone M, Day A, Nickerson E, Stajich JE, Harris TW, Arva A, Lewis S. The generic genome browser: a building block for a model organism system database. Genome Res 2002, 12:1599-1610. 10.1101/gr.403602, 187535, 12368253.
7. Hubbard T, Barker D, Birney E, Cameron G, Chen Y, Clark L, Cox T, Cuff J, Curwen V, Down T, Durbin R, Eyras E, Gilbert J, Hammond M, Huminiecki L, Kasprzyk A, Lehvaslaiho H, Lijnzaad P, Melsopp C, Mongin E, Pettett R, Pocock M, Potter S, Rust A, Schmidt E, Searle S, Slater G, Smith J, Spooner W, Stabenau A, Stalker J, Stupka E, Ureta-Vidal A, Vastrik I, Clamp M. The Ensembl genome database project. Nucleic Acids Res 2002, 30(1):38-41. 10.1093/nar/30.1.38, 99161, 11752248.
8. Dombrowski SM, Maglott D. Using the map viewer to explore genomes. The NCBI Handbook 2002, National Center for Biotechnology Information.
9. Skinner ME, Uzilov AV, Stein LD, Mungall CJ, Holmes IH. JBrowse: a next-generation genome browser. Genome Res 2009, 19:1630-1638. 10.1101/gr.094607.109, 2752129, 19570905.
10. Yang H, Wang J, Didion JP, Buus RJ, Bell TA, Welsh CE, Bonhomme F, Yu AH, Nachman MW, Pialek J, Tucker P, Boursot P, McMillan L, Churchill GA, Villena FPM. Subspecific origin and haplotype diversity in the laboratory mouse. Nat Genet 2011, 43:648-655. 10.1038/ng.847, 3125408, 21623374.
11. Yang H, Ding Y, Hutchins LN, Szatkiewicz J, Bell TA, Paigen BJ, Graber JH, Villena FPM, Churchill GA. A customized and versatile high-density genotyping array for the mouse. Nat Methods 2009, 6:663-666. 10.1038/nmeth.1359, 2735580, 19668205.
12. Hsu F, Kent WJ, Clawson H, Kuhn RM, Diekhans M, Haussler D. The UCSC known genes. Bioinformatics 2006, 22(9):1036-1046. 10.1093/bioinformatics/btl048, 16500937.
13. Didion JP, Yang H, Sheppard K, Fu C, McMillan L, Villena FPM, Churchill GA. Discovery of novel variants in genotyping arrays significantly improves genotype retention and corrects ascertainment bias. BMC Genomics
14. Wang J, Moore KJ, Zhang Q, Villena FPM, Wang W, McMillan L. Genome-wide compatible SNP intervals and their properties. Proceedings of ACM International Conference on Bioinformatics and Computational Biology 2010,
15. Wang JR, Villena FPM, Lawson HA, Cheverud JM, Churchill GA, McMillan L. Imputation of SNPs in inbred mice using local phylogeny. Genetics 2011,
16. Aylor DL, Valdar W, Foulds-Mathes W, Buus RJ, Verdugo RA, Baric RS, Ferris MT, Frelinger JA, Heise M, Frieman MB, Gralinski LE, Bell TA, Didion JD, Hua K, Nehrenberg DL, Powell CL, Steigerwalt J, Xie Y, Kelada SNP, Collins F, Yang IV, Schwartz DA, Branstetter LA, Chesler EJ, Miller DR, Spence J, Liu EY, McMillan L, Sarkar A, Wang J, Wang W, Zhang Q, Broman KW, Korstanje R, Durrant C, Mott R, Iraqi FA, Pomp D, Threadgill D, Villena FPM, Churchill GA. Genetic analysis of complex traits in the emerging Collaborative Cross. Genome Res 2011, 21:1213-1222. 10.1101/gr.111310.110, 3149489, 21406540.
17. Collaborative Cross Consortium The genome architecture of the Collaborative Cross mouse genetic reference population. Genetics 2011, Collaborative Cross Consortium.