Genome-wide DNA polymorphism analyses using VariScan

BMC Bioinformatics

Volumn 7, Issue , 2006, Pages

  Hutter, Stephan ^a,b   Vilella, Albert J ^a   Rozas, Julio ^a  

^a UNIVERSITY OF BARCELONA   (Spain)

^b UNIVERSITY OF MUNICH   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

COMPREHENSIVE ANALYSIS; DNA POLYMORPHISM; EXPLORATORY ANALYSIS; GENOME ANNOTATION; GENOME PROJECTS; HIGH-THROUGHPUT; NATURAL SELECTION; NUCLEOTIDE VARIATION;

DATA VISUALIZATION; DNA SEQUENCES; POPULATION STATISTICS; USER INTERFACES;

GENES;

ARTICLE; COMPUTER INTERFACE; COMPUTER PROGRAM; COMPUTER SIMULATION; CONTROLLED STUDY; DNA POLYMORPHISM; DNA SEQUENCE; GENETIC ALGORITHM; GENETIC ANALYSIS; GENOME ANALYSIS; HIGH THROUGHPUT SCREENING; HUMAN; MOUSE; NONHUMAN; ALGORITHM; ANIMAL; COMPUTER GRAPHICS; GENETIC POLYMORPHISM; GENETIC SELECTION; GENOME; NUCLEOTIDE SEQUENCE; PROCEDURES; SEQUENCE ALIGNMENT; SINGLE NUCLEOTIDE POLYMORPHISM;

ALGORITHMS; ANIMALS; BASE SEQUENCE; COMPUTER GRAPHICS; GENOME; HUMANS; MICE; POLYMORPHISM, GENETIC; POLYMORPHISM, SINGLE NUCLEOTIDE; SELECTION, GENETIC; SEQUENCE ALIGNMENT; SOFTWARE; USER-COMPUTER INTERFACE;

EID: 33749156386     PISSN: 14712105     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-7-409     Document Type: Article

References (52)

1. Hudson RR, Kreitman M, Aguadé M: A test of neutral molecular evolution based on nucleotide data. Genetics 1987, 116:153-159.
2. McDonald JH, Kreitman M: Adaptive protein evolution at the Adh locus in Drosophila. Nature 1991, 351:652-654.
3. Hughes AL, Yeager M: Natural selection at major histocompatibility complex loci of vertebrates. Annu Rev Genet 1998, 32:415-435.
4. Kimura M: The Neutral Theory of Molecular Evolution Cambridge: Cambridge University Press; 1983.
5. Kingman JFC: On the genealogy of large populations. J Appl Prob 1982, 19A-27-43.
6. Hudson RR: Gene genealogies and the coalescent process. Oxf Surv Evol Biol 1990, 7:1-44.
7. Sabeti PC, Reich DE, Higgins JM, Levine HZ, Richter DJ, Schaffner SF, Gabriel SB, Platko JV, Patterson NJ, McDonald GJ, Ackerman HC, Campbell SJ, Altshuler D, Cooper R, Kwiatkowski D, Ward R, Lander ES: Detecting recent positive selection in the human genome from haplotype structure. Nature 2002, 419:832-837.
8. Quesada H, Ramírez UEM, Rozas J, Aguadé M: Large-Scale Adaptive Hitchhiking upon High Recombination. Genetics 2003, 165:895-900.
9. Mekel-Bobrov N, Gilbert SL, Evans PD, Vallender EJ, Anderson JR, Hudson RR, Tishkoff SA, Lahn BT: Ongoing Adaptive Evolution of ASPM, a Brain Size Determinant in Homo sapiens. Science 2005, 309:1720-1722.
10. Orengo DJ, Aguadé M: Detecting the Footprint of Positive Selection in a European Population of Drosophila melanogaster. Multilocus Pattern of Variation and Distance to Coding Regions. Genetics 2004, 167:1759-1766.
11. Haddrill PR, Thornton KR, Charlesworth B, Andolfatto P: Multilocus patterns on nucleotide variability and the demographic and selection history of Drosophila melanogaster populations. Genome Res 2005, 15:790-799.
12. Nordborg M, Hu TT, Ishino Y, Jhaveri J, Toomajian C, Zheng H, Bakker E, Calabrese P, Gladstone J, Goyal R, Jakobsson M, Kim S, Morozov Y, Padhukasahasram B, Plagnol V, Rosenberg NA, Shah C, Wall JD, Wang J, Zhao K, Kalbfleisch T, Schulz V, Kreitman M, Bergelson J: The pattern of polymorphism in Arabidopsis thaliana. PLoS Biology 2005, 3:1289-1299.
13. Kreitman M: Nucleotide polymorphism at the alcohol dehydrogenase locus of Drosophila melanogaster. Nature 1983, 304:412-417.
14. Andolfatto P: Adaptive evolution of non-coding DNA in Drosophila. Nature 2005, 437:1149-1152.
15. MacDonald SJ, Long AD: Identifying Signatures of Selection at the Enhancer of split Neurogenic Gene Complex in Drosophila. Mol Biol Evol 2005, 22:607-619.
16. HapMap web site [http://www.genome.gov/10001688]
17. ENCODE web site [http://www.genome.gov/10005107]
18. Sim Yak web site [http://www.dpgp.ogr/simyak/]
19. DPGP web site [http://www.dpgp.org/aboutdpgp/]
20. Mouse Genome Resequencing Project web site [http://www.niehs.nih.gov/crg/ cprc.htm]
21. Filatov DA: ProSeq: A software for preparation and evolutionary analysis of DNA sequence data sets. Mol Ecol Notes 2002, 2:621-624.
22. Rozas J, Sánchez-Del Barrio JC, Messeguer X, Rozas R: DnaSP, DNA polymorphism analyses by the coalescent and other methods. Bioinformatics 2003, 19:2496-2497.
23. Excoffier L, Laval G, Schneider S: Arlequin (version 3): An integrated software package for population genetics data analysis. Evol Bioinformatics Online 2005, 1:47-50.
24. Vilella AJ, Blanco-Garcia A, Hutter S, Rozas J: VariScan: Analysis of evolutionary patterns from large-scale DNA sequence polymorphism data. Bioinformatics 2005, 21:2791-2793.
25. Rozas J, Rozas R. DnaSP, DNA sequence polymorphism: an interactive program for estimating Population Genetics parameters from DNA sequence data. Comput Appl Biosci 1995, 11:621-625.
26. Arneodo A, Bacry E, Graves P, Vand Muzy JF: Characterizing long-range correlations in DNA sequences from wavelet analysis. Phys Rev Lett 1995, 74:3293-3296.
27. Mallat SG: A theory for multiresolution signal decomposition: the wavelet representation. IEEE Trans Pattern Anal Mach Intell 1989, 11:674-693.
28. Liò P, Wavelets in bioinformatics and computational biology: state of art and perspectives. Bioinformatics 2003, 19:2-9.
29. LastWave v2.0 software web site [http://www.cmap.polytechnique.fr/~bacry/ LastWave/]
30. Nei M: Molecular Evolutionary Genetics New York: Columbia University Press; 1987.
31. Rosenberg NA, Nordborg M: Genealogical trees, coalescent theory, and the analysis of genetic polymorphisms. Nat Rev Genet 2002, 3:380-390.
32. Depaulis F, Veuille M: Neutrality tests based on the distribution of haplotypes under an infinite-site model. Mol Biol Evol 1998, 15:1788-1790.
33. Lewontin RC: The interaction of selection and linkage. I General considerations: heterotic models. Genetics 1964, 49:49-67.
34. Hill WG, Robertson A: Linkage disequilibriurn in finite populations. Theor Appl Genet 1968, 38:226-231.
35. Kelly JK: A test of neutrality based on interlocus associations. Genetics 1997, 146:1197-1206.
36. Tajima F: Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 1989, 123:585-595.
37. Fu YX, Li WH: Statistical tests of neutrality of mutations. Genetics 1993, 133:693-709.
38. Fu YX: Statistical tests of neutrality of mutations against population growth, hitchhiking and background selection. Genetics 1997, 147:915-925.
39. Fay JC, Wu CI: Hitchhiking under positive Darwinian selection. Genetics 2000, 155:1405-1413.
40. Patil N, Berno AJ, Hinds DA, Barrett WA, Doshi JM, Hacker CR, Kautzer CR, Lee DH, Marjoribanks C, McDonough DP, Nguyen BTN, Norris MC, Sheehan JB, Shen N, Stern D, Stokowski RP, Thomas DJ, Trulson MO, Vyas KR, Frazer KA, Fodor SPA, Cox DR. Blocks of Limited Haplotype Diversity Revealed by High-Resolution Scanning of Human Chromosome 21. Science 2001, 294:1719-1723.
41. GFF file format [http://www.sanger.ac.uk/Software/formats/GFF/]
42. VISTA server [http://genome.lbl.gov/vista/index.shtml]
43. Daubechies I: Ten lectures on wavelets. CBMS-NSF Regional Conference Series in Applied Mathematics. Philadelphia 1992.
44. Liò P, Vanucci M: Finding pathogenicity islands and gene transfer events in genome data. Bioinformatics 2000, 16:932-940.
45. 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.
46. 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.
47. Innan H, Padhukasahasram B, Nordborg M: The Pattern of Polymorphism on Human Chromosome 21. Genome Res 2003, 13:1158-1168.
48. Kaplan NL, Hudson RR, Langley CH: The "hitchhiking effect" revisited. Genetics 1989, 123:887-899.
49. Kim Y, Stephan W: Detecting a local signature of genetic hitchhiking along a recombining chromosome. Genetics 2002, 160:765-777.
50. Hudson RR: Generating samples under a Wright-Fisher neutral model of genetic variation. Bioinformatics 2002, 18:337-338.
51. Tajima F. Determination of window size for analyzing DNA sequences. J Mol Evol 1991, 33:470-473.
52. Fares MA, Elena SF, Ortiz J, Moya A, Barrio E: A Sliding Window-Based Method to Detect Selective Constraints in Protein-Coding Genes and Its Application to RNA Viruses. J Mol Evol 2002, 55:509-521.