A practical guide to orient yourself in the labyrinth of genome databases

Human Molecular Genetics

Volumn 7, Issue 10, 1998, Pages 1641-1648

  Borsani, Giuseppe ^a   Ballabio, Andrea ^a,b   Banfi, Sandro ^a  

^a TELETHON INSTITUTE OF GENETICS AND MEDICINE TIGEM   (Italy)

^b VITA SALUTE SAN RAFFAELE UNIVERSITY   (Italy)

Author keywords

[No Author keywords available]

Indexed keywords

DNA;

ARTICLE; DATA BASE; DNA SEQUENCE; GENOME; INFORMATION RETRIEVAL; INTERNET; MEDICAL GENETICS; PRIORITY JOURNAL;

CHROMOSOME MAPPING; CLONING, MOLECULAR; COMPUTATIONAL BIOLOGY; DATABASES, FACTUAL; DNA, COMPLEMENTARY; EXPRESSED SEQUENCE TAGS; GENETIC DISEASES, INBORN; GENOME, HUMAN; HUMAN GENOME PROJECT; HUMANS; INTERNET; SEQUENCE ANALYSIS, DNA;

EID: 0031658645     PISSN: 09646906     EISSN: None     Source Type: Journal    
DOI: 10.1093/hmg/7.10.1641     Document Type: Article

References (34)

1. McKusick, V.A., Francomano, C. and Antonarakis, S.E. (1995) Catalogs of autosomal dominant, autosomal recessive, and X-linked phenotypes. In Mendelian Inheritance in Man. Johns Hopkins University Press, Baltimore, MD.
2. Collins, F.S. (1992) Positional cloning: let's not call it reverse anymore. Nature Genet., 1, 3-6.
3. Ballabio, A. (1993) The rise and fall of positional cloning? Nature Genet., 3, 277-279.
4. Collins, F.S. (1995) Positional cloning moves from perditional to traditional. Nature Genet., 9, 347-350.
5. Green, E.D., Cox, D.R. and Myers, R.M. (1995). The human genome project and its impact on the study of human disease. In Scriver, C.R., Beaudet, A.L., Sly, W.S. and Valle, D. (eds), The Metabolic and Molecular Bases of Inherited Disease. McGraw-Hill, New York, Vol. I, pp. 401-436.
6. Guyer, M.S. and Collins, F.S. (1995) How is the Human Genome Project doing, and what have we learned so far? Proc. Natl. Acad. Sci. USA, 92, 10841-10848.
7. Chumakov, I.M., Rigault, P., Le Gall, I., Bellanné-Chantelot, C., Billault, A., Guillou, S., Soularue, P., Guasconi, G., Poullier, E., Gros, I., Belova, M., Sambucy, J.-L., Susini, L., Gervy, P., Gilbert, F., Beaufils, S., Bui, H., Massart, C., De Tand, M.-F., Dukasz, F., Lecoulant, S., Ougen, P., Perrot, V., Saumier, M., Soravito, C., Bahouayila, R., Cohen-Akenine, A., Barillot, E., Bertrand, S., Codani, J.-J., Caterina, D., Georges, I., Lacroix, B., Lucotte, G., Sahbatou, M., Schmit, C., Sangouard, M., Tubacher, E., Dib, C., Fauré, S., Fizames, C., Gyapay, G., Millasseau, P., NGuyen, S., Muselet, D., Vignal, A., Morissette, J., Menninger, J., Leiman, J., Desai, T., Banks, A., Bray-Ward, P., Ward, D., Hudson, T., Gerety, S., Foote, S., Stein, L., Page, D.C., Lander, E.S., Weissenbach, J., Le Paslier, D. and Cohen, D. (1995) A YAC contig map of the human genome. Nature, 377 (suppl.), 175-183.
8. Dib, C., Fauré, S., Fizames, C., Samson, D., Drouot, N., Vignal, A., Millasseau, P., Marc, S., Hazan, J., Seboun, E., Lathrop, M., Gyapay, G., Morissette, J. and Weissenbach, J. (1996) A comprehensive genetic map of the human genome based on 5,264 microsatellites. Nature, 380, 152-154.
9. Hudson, T.J., Stein, L.D., Gerety, S.S., Ma, J., Castle, A.B., Silva, J., Slonim, D.K., Baptista, R., Kruglyak, L., Xu, S.-H., Hu, X., Colbert, A.M.E., Rosenberg, C., Reeve-Daly, M.P., Rozen, S., Hui, L., Wu, X., Vestergaard, C., Wilson, K.M., Bae, J.S., Maitra, S., Ganiatsas, S., Evans, C.A., DeAngelis, M.M., Ingalls, K.A., Nahf, R.W., Horton, L.T. Jr, Anderson, M.O., Collymore, A.J., Ye, W., Kouyoumjian, V., Zemsteva, I.S., Tam, J., Devine, R., Courtney, D.F., Renaud, M.T., Nguyen, H., O-Connor, T.J., Fizames, C., Fauré, S., Gyapay, G., Dib, C., Morissette, J., Orlin, J.B., Birren, B.W., Goodman, N., Weissenbach, J., Hawkins, T.L., Foote, S., Page, D.C. and Lander, E.S. (1995) An STS-based map of the human genome. Science, 270, 1945-1954.
10. Adams, M.D., Kerlavage, A.R., Fleischmann, R.D., Fuldner, R.A., Bult, C.J., Lee, N.H., Kirkness, E.F., Weinstock, K.G., Gocayne, J.D., White, O., Sutton, G., Blake, J.A., Brandon, R.C., Chiu, M.-W., Clayton, R.A., Cline, R.T., Cotton, M.D., Earle-Hughes, J., Fine, L.D., FitzGerald, L.M., FitzHugh, W.M., Fritchman, J.L., Geoghagen, N.S.M., Glodek, A., Gnehm, C.L., Hanna, M.C., Hedblom, E., Hinkle, P.S. Jr, Kelley, J.M., Klimek, K.M., Kelley, J.C., Liu, L.-I., Marmaros, S.M., Merrick, J.M., Moreno-Palanques, R.F., McDonald, L.A., Nguyen, D.T., Pellegrino, S.M., Phillips, C.A., Ryder, S.E., Scott, J.L., Saudek, D.M., Shirley, R., Small, K.V., Spriggs, T.A., Utterback, T.R., Weidman, J.F., Li, Y., Barthlow, R., Bednarik, D.P., Cao, L., Cepeda, M.A., Coleman, T.A., Collins, E.-J., Dimke, D., Feng, P., Ferrie, A., Fischer, C., Hastings, G.A., He, W.-W., Hu, J.-S., Huddleston, K.A., Greene, J.M., Gruber, J., Hudson, P., Kim, A., Kozak, D.L., Kunsch, C., Ji, H., Li, H., Meissner, P.S., Olsen, H., Raymond, L., Wei, Y.-F., Wing, J., Xu, C., Yu, G.-L., Ruben, S.M., Dillon, P.J., Fannon, M.R., Rosen, C.A., Haseltine, W.A., Fields, C., Fraser, C.M. and Venter, J.C. (1995) Initial assessment of human gene diversity and expression patterns based upon 83 million nucleotides of cDNA sequence. Nature. 377 (suppl.), 3-17.
11. Hillier, L., Lennon, G., Becker, M., Bonaldo, M.F., Chiapelli, B., Chissoe, S., Dietrich, N., DuBuque, T., Favello, A., Gish, W., Hawkins, M., Hultman, M., Kucaba, T., Lacy, M., Le, M., Le, N., Mardis, E., Moore, B., Morris, M., Parsons, J., Prange, C., Rifkin, L., Rohlfing, T., Schellenberg, K., Bento Soares, M., Tan, F., Thierry-Meg, J., Trevaskis, E., Underwood, K., Wohldman, P., Waterston, R., Wilson, R. and Marra, M. (1996) Generation and analysis of 280,000 human expressed sequence tags. Genome Res., 6, 807-828.
12. Strausberg, R.L., Dahl, C.A. and Klausner, R.D. (1997) New opportunities for uncovering the molecular basis of cancer. Nature Genet., 16 (suppl.), 415-516.
13. Fasman, K., Letovsky, S., Li, P., Cottingham, R. and Kingsbury, D. (1997) The GDB Human Genome Database Anno 1997. Nucleic Acids Res., 25, 72-81.
14. Collins, A., Frezal, J., Teague, J. and Morton, N. (1996) A metric map of humans: 23,500 loci in 850 bands. Proc. Natl Acad. Sci. USA, 93, 14771-14775.
15. Benson, D., Boguski, M., Lipman, D., Ostell, J. and Ouellette, B. (1998) GenBank. Nucleic Acids Res., 26, 1-7.
16. Schuler, G., Epstein, J., Ohkawa, H. and Kans, J. (1996) Entrez: molecular biology database and retrieval system. Methods Enzymol., 266, 141-162.
17. Altschul, S.F., Gish, W., Miller, W., Myers, E.W. and Lipman, D.J. (1990) Basic local alignment search tool. J. Mol. Biol., 215, 403-410.
18. Altschul, S.F., Madden, T.L., Schäffer A.A., Zhang, J., Zhang, Z., Miller, W. and Lipman, D.J. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res., 25, 3389-3402.
19. Boguski, M.S., Lowe, T.M.J. and Tolstoshev, C.M. (1993) dbEST - database for 'expressed sequence tags'. Nature Genet., 4, 332-333.
20. Ouellette, B. and Boguski, M. (1997) Database divisions and homology search files: a guide for the perplexed. Genome Res., 7, 952-955.
21. Boguski, M.S. and Schuler, G.D. (1995) ESTablishing a human transcript map. Nature Genet., 10, 369-373.
22. Schuler, G.D., Boguski, M.S., Stewart, E.A., Stein, L.D., Gyapay, G., Rice, K., White, R.E., Rodriguez-Tomé, P., Aggarwal, A., Bajorek, E., Bentolila, S., Birren, B.B., Butler, A., Castle, A.B., Chiannilkulchai, N., Chu, A., Clee, C., Cowles, S., Day, P.J.R., Dibling, T., Drouot, N., Dunham, I., Duprat, S., East, C., Edwards, C., Fan, J.-B., Fang, N., Fizames, C., Garrett, C., Green, L., Hadley, D., Harris, M., Harrison, P., Brady, S., Hicks, A., Holloway, E., Hui, L., Hussain, S., Louis-Dit-Sully, C., Ma, J., MacGilvery, A., Mader, C., Maratukulam, A., Mantise, T.C., McKusick, K.B., Morissette, J., Mungall, A., Muselet, D., Nusbaum, H.C., Page, D.C., Peck, A., Perkins, S., Piercy, M., Qin, F., Quackenbush, J., Ranby, S., Reif, T., Rozen, S., Sanders, C., She, X., Silva, J., Slonim, D.K., Soderlund, C., Sun, W.-L., Tabar, P., Thangarajah, T., Vega-Czarny, N., Vollrath, D., Voyticky, S., Wilmer, T., Wu, X., Adams, M.D., Auffray, C., Walter, N.A.R., Brandon, R., Dehejia, A., Goodfellow, P.N., Houlgatte, R., Hudson, J.R. Jr, Ide, S.E., Iorio, K.R., Lee, W.Y., Seki, N., Nagase, T., Ishikawa, K., Nomura, N., Phillips, C., Polymeropoulos, M.H., Sandusky, M., Schmitt, K., Berry, R., Swanson, K., Torres, R., Venter, J.C., Sikela, J.M., Beckmann, J.S., Weissenbach, J., Myers, R.M., Cox, D.R., James, M.R. et al. (1996) A gene map of the human genome. Science, 274, 540-546.
23. Cox, D.R., Burmeister, M., Price, E.R., Kim, S. and Myers, R.M. (1990) Radiation hybrid mapping: a somatic cell genetic method for constructing high-resolution maps of mammalian chromosomes. Science, 250, 245-250.
24. Lijnzaad, P., Helgesen, C. and Rodriguez, T.P. (1998) The Radiation Hybrid Database. Nucleic Acids Res., 26, 102-105.
25. Haravuori, H., Makela, B.P., Udd, B., Partanen, J., Pulkkinen, L., Somer, H. and Peltonen, L. (1998) Assignment of the tibial muscular dystrophy locus to chromosome 2q31. Am. J. Hum. Genet., 62, 620-626.
26. Banfi, S., Guffanti, A. and Borsani, G. (1998) How to get the best of dbEST. Trends Genet., 14, 80-81.
27. Huang, X. (1996) An improved sequence assembly program. Genomics, 33, 21-31.
28. Gill, R.W., Hodgman, T.C., Littler, C.B., Oxer, M.D., Montgomery, D.S., Taylor, S. and Sanseau, P. (1997) A new dynamic toll to perform assembly of expressed sequence tags (ESTs). CABIOS, 13, 453-457.
29. Sauer, C.G., Gehrig, A., Warneke-Wittstock, R., Marquardt, A., Ewing, C.C., Gibson, A., Lorenz, B., Jurklies, B. and Weber, B.H.F. (1997) Positional cloning of the gene associated with X-linked juvenile retinoschisis. Nature Genet., 17, 164-170.
30. Miki, Y., Swensen, J., Shattuck, E.D., Futreal, P., Harshman, K., Tavtigian, S., Liu, Q., Cochran, C., Bennett, L., Ding, W. et al. (1994) A strong candidate for the breast and ovarian cancer susceptibility gene BRCA1. Science, 266, 66-71.
31. Harris, N. (1997) Genotator a workbench for sequence annotation. Genome Res., 7, 754-762.
32. Banfi, S., Borsani, G., Rossi, E., Bernard, L., Guffanti, A., Rubboli, F., Marchitiello, A., Giglio, S., Coluccia, E., Zollo, M., Zuffardi, O. and Ballabio, A. (1996) Identification and mapping of human cDNAs homologous to Drosophila mutant genes through EST database searching. Nature Genet., 13, 167-174.
33. Rampazzo, A., Nava, A., Danieli, G., Buja. G., Daliento, L., Fasoli, G., Scognamiglio, R., Corrado, D. and Thiene, G. (1994) The gene for arrhythmogenic right ventricular cardiomyopathy maps to chromosome 14q23-q24. Hum. Mol. Genet., 3, 959-962.
34. Moross, T., Vaithilingam, S., Styles, S. and Gardner, H. (1984) Autosomal dominant anterior polar cataracts associated with a familial 2;14 translocation. J. Med. Genet., 21, 52-53.