Drosophila polymorphism database (DPDB) a portal for nucleotide polymorphism in Drosophila

Fly

Volumn 1, Issue 4, 2007, Pages 205-211

  Casillas, Sònia ^a   Egea, Raquel ^a   Petit, Natalia ^a   Bergman, Casey M ^b   Barbadilla, Antonio ^a  

^a UNIVERSITAT AUTÒNOMA DE BARCELONA   (Spain)

^b UNIVERSITY OF MANCHESTER   (United Kingdom)

Author keywords

Bioinformatics of genetic diversity; Database; DNA polymorphism; Drosophila; Large scale analyses; Nucleotide variation; Population genetics

Indexed keywords

ANIMAL; ARTICLE; DROSOPHILA MELANOGASTER; GENETIC DATABASE; GENETIC POLYMORPHISM; GENETICS; GENOME; INTERNET;

ANIMALS; DATABASES, GENETIC; DROSOPHILA MELANOGASTER; GENOME, INSECT; INTERNET; POLYMORPHISM, GENETIC;

EID: 55249120779     PISSN: 19336934     EISSN: 19336942     Source Type: Journal    
DOI: 10.4161/fly.5043     Document Type: Article

References (38)

1. Lewontin RC. The Genetic Basis of Evolutionary Change. New York: Columbia University Press, 1974.
2. Lewontin RC. Directions in evolutionary biology. Annu Rev Genet 2002; 36:1-18.
3. Kreitman M. Nucleotide polymorphism at the alcohol dehydrogenase locus of Drosophila melanogaster. Nature 1983; 304:412-7.
4. Li WH, Gu Z, Wang H, Nekrutenko A. Evolutionary analyses of the human genome. Nature 2001; 409:847-9.
5. Aquadro CF, Bauer DuMont V, Reed FA. Genome-wide variation in the human and fruitfly: A comparison. Curr Opin Genet Dev 2001; 11:627-34.
6. Powell JR. Progress and Prospects in Evolutionary Biology: The Drosophila Model. NY: Oxford University Press, 1997.
7. Andolfatto P. Adaptive evolution of non-coding DNA in Drosophila. Nature 2005; 437:1149-52.
8. Glinka S, Ometto L, Mousset S, Stephan W, De Lorenzo D. Demography and natural selection have shaped genetic variation in Drosophila melanogaster: A multi-locus approach. Genetics 2003; 165:1269-78.
9. Ometto L, Glinka S, De Lorenzo D, Stephan W. Inferring the eff-ects of demography and selection on Drosophila melanogaster populations from a chromosome-wide scan of DNA variation. Mol Biol Evol 2005; 22:2119-30.
10. Orengo DJ, Aguade 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; 167:1759-66.
11. Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Wheeler DL. GenBank. Nucleic Acids Res 2007; 35:D21-5.
12. Pandey A, Lewitter F. Nucleotide sequence databases: A gold mine for biologists. Trends Biochem Sci 1999; 24:276-80.
13. Casillas S, Petit N, Barbadilla A. DPDB: A database for the storage, representation and analysis of polymorphism in the Drosophila genus. Bioinformatics 2005; 21:ii26-ii30.
14. Casillas S, Barbadilla A. PDA: A pipeline to explore and estimate polymorphism in large DNA databases. Nucleic Acids Res 2004; 32:W166-9.
15. Casillas S, Barbadilla A. PDA v.2: Improving the exploration and estimation of nucleotide polymorphism in large datasets of heterogeneous DNA. Nucleic Acids Res 2006; 34: W632-4.
16. Matthews KA, Kaufman TC, Gelbart WM. Research resources for Drosophila: The expanding universe. Nat Rev Genet 2005; 6:179-93.
17. Galperin MY. The molecular biology database collection: 2007 update. Nucleic Acids Res 2007; 35:D3-4.
18. Begun DJ, Aquadro CF. Levels of naturally occurring DNA polymorphism correlate with recombination rates in D. melanogaster. Nature 1992; 356:519-20.
19. Betancourt AJ, Presgraves DC. Linkage limits the power of natural selection in Drosophila. Proc Natl Acad Sci USA 2002; 99:13616-20.
20. Nelson CE, Hersh BM, Carroll SB. The regulatory content of intergenic DNA shapes genome architecture. Genome Biol 2004; 5:R25.
21. Petit N, Casillas S, Ruiz A, Barbadilla A. Protein polymorphism is negatively correlated with conservation of intronic sequences and complexity of expression patterns in Drosophila melanogaster. J Mol Evol 2007; 64:511-8.
22. Wheeler DL, Barrett T, Benson DA, Bryant SH, Canese K, Chetvernin V, Church DM, DiCuccio M, Edgar R, Federhen S, Geer LY, Kapustin Y, Khovayko O, Landsman D, Lipman DJ, Madden TL, Maglott DR, Ostell J, Miller V, Pruitt KD, Schuler GD, Sequeira E, Sherry ST, Sirotkin K, Souvorov A, Starchenko G, Tatusov RL, Tatusova TA, Wagner L, Yaschenko E. Database resources of the national center for biotechnology information. Nucleic Acids Res 2007; 35:D5-12.
23. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, Harris MA, Hill DP, Issel-Tarver L, Kasarskis A, Lewis S, Matese JC, Richardson JE, Ringwald M, Rubin GM, Sherlock G. Gene ontology: Tool for the unification of biology: The gene ontology consortium. Nat Genet 2000; 25:25-9.
24. Crosby MA, Goodman JL, Strelets VB, Zhang P, Gelbart WM. FlyBase: Genomes by the dozen. Nucleic Acids Res 2007; 35:D486-91.
25. Adams MD, Celniker SE, Holt RA, Evans CA, Gocayne JD, Amanatides PG, Scherer SE, Li PW, Hoskins RA, Galle RF, George RA, Lewis SE, Richards S, Ashburner M, Henderson SN, Sutton GG, Wortman JR, Yandell MD, Zhang Q, Chen LX, Brandon RC, Rogers YH, Blazej RG, Champe M, Pfeiffer BD, Wan KH, Doyle C, Baxter EG, Helt G, Nelson CR, Gabor GL, Abril JF, Agbayani A, An HJ, Andrews-Pfannkoch C, Baldwin D, Ballew RM, Basu A, Baxendale J, Bayraktaroglu L, Beasley EM, Beeson KY, Benos PV, Berman BP, Bhandari D, Bolshakov S, Borkova D, Botchan MR, Bouck J, Brokstein P, Brottier P, Burtis KC, Busam DA, Butler H, Cadieu E, Center A, Chandra I, Cherry JM, Cawley S, Dahlke C, Davenport LB, Davies P, de Pablos B, Delcher A, Deng Z, Mays AD, Dew I, Dietz SM, Dodson K, Doup LE, Downes M, Dugan-Rocha S, Dunkov BC, Dunn P, Durbin KJ, Evangelista CC, Ferraz C, Ferriera S, Fleischmann W, Fosler C, Gabrielian AE, Garg NS, Gelbart WM, Glasser K, Glodek A, Gong F, Gorrell JH, Gu Z, Guan P, Harris M, Harris NL, Harvey D, Heiman TJ, Hernandez JR, Houck J, Hostin D, Houston KA, Howland TJ, Wei MH, Ibegwam C, Jalali M, Kalush F, Karpen GH, Ke Z, Kennison JA, Ketchum KA, Kimmel BE, Kodira CD, Kraft C, Kravitz S, Kulp D, Lai Z, Lasko P, Lei Y, Levitsky AA, Li J, Li Z, Liang Y, Lin X, Liu X, Mattei B, McIntosh TC, McLeod MP, McPherson D, Merkulov G, Milshina NV, Mobarry C, Morris J, Moshrefi A, Mount SM, Moy M, Murphy B, Murphy L, Muzny DM, Nelson DL, Nelson DR, Nelson KA, Nixon K, Nusskern DR, Pacleb JM, Palazzolo M, Pittman GS, Pan S, Pollard J, Puri V, Reese MG, Reinert K, Remington K, Saunders RD, Scheeler F, Shen H, Shue BC, Siden-Kiamos I, Simpson M, Skupski MP, Smith T, Spier E, Spradling AC, Stapleton M, Strong R, Sun E, Svirskas R, Tector C, Turner R, Venter E, Wang AH, Wang X, Wang ZY, Wassarman DA, Weinstock GM, Weissenbach J, Williams SM, Woodage T, Worley KC, Wu D, Yang S, Yao QA, Ye J, Yeh RF, Zaveri JS, Zhan M, Zhang G, Zhao Q, Zheng L, Zheng XH, Zhong FN, Zhong W, Zhou X, Zhu S, Zhu X, Smith HO, Gibbs RA, Myers EW, Rubin GM, Venter JC. The genome sequence of Drosophila melanogaster. Science 2000; 287:2185-95.
26. Chenna R, Sugawara H, Koike T, Lopez R, Gibson TJ, Higgins DG, Thompson JD. Multiple sequence alignment with the Clustal series of programs. Nucleic Acids Res 2003; 31:3497-500.
27. Edgar RC. MUSCLE: Multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 2004; 32:1792-7.
28. Notredame C, Higgins DG, Heringa J. T-Coffee: A novel method for fast and accurate multiple sequence alignment. J Mol Biol 2000; 302:205-17.
29. Casillas S, Barbadilla A, Bergman CM. Purifying selection maintains highly conserved noncoding sequences in Drosophila. Mol Biol Evol 2007.
30. Kent WJ. BLAT-the BLAST-like alignment tool. Genome Res 2002; 12:656-64.
31. Hinrichs AS, Karolchik D, Baertsch R, Barber GP, Bejerano G, Clawson H, Diekhans M, Furey TS, Harte RA, Hsu F, Hillman-Jackson J, Kuhn RM, Pedersen JS, Pohl A, Raney BJ, Rosenbloom KR, Siepel A, Smith KE, Sugnet CW, Sultan-Qurraie A, Thomas DJ, Trumbower H, Weber RJ, Weirauch M, Zweig AS, Haussler D, Kent WJ. The UCSC genome browser database: Update 2006. Nucleic Acids Res 2006; 34:D590-8.
32. Egea R, Casillas S, Fernandez E, Senar MA, Barbadilla A. MamPol: A database of nucleotide polymorphism in the Mammalia class. Nucleic Acids Res 2007; 35:D624-9.
33. McGinnis S, Madden TL. BLAST: At the core of a powerful and diverse set of sequence analysis tools. Nucleic Acids Res 2004; 32:W20-5.
34. Clamp M, Cuff J, Searle SM, Barton GJ. The Jalview Java alignment editor. Bioinformatics 2004; 20:426-7.
35. Charlesworth B. Background selection and patterns of genetic diversity in Drosophila melanogaster. Genet Res 1996; 68:131-49.
36. Caceres M, Barbadilla A, Ruiz A. Recombination rate predicts inversion size in Diptera. Genetics 1999; 153:251-9.
37. Andolfatto P. Contrasting patterns of X-linked and autosomal nucleotide variation in Drosophila melanogaster and Drosophila simulans. Mol Biol Evol 2001; 18:279-90.
38. McDonald JH, Kreitman M. Adaptive protein evolution at the Adh locus in Drosophila. Nature 1991; 351:652-4.