JESAM: CORBA software components to create and publish EST alignments and clusters

Bioinformatics

Volumn 16, Issue 4, 2000, Pages 313-325

  Parsons, J D ^a,b   Rodriguez Tome P ^a  

^a WELLCOME TRUST SANGER INSTITUTE   (United Kingdom)

^b Cereon Genomics   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

MESSENGER RNA;

ARTICLE; COMPUTER INTERFACE; DATA BASE; EUKARYOTE; EXPRESSED SEQUENCE TAG; GENE MAPPING; GENE SEQUENCE; GENETIC POLYMORPHISM; GENOME; INTERNET; INTERPERSONAL COMMUNICATION; MASS SPECTROMETER; PRIORITY JOURNAL; TEAMWORK;

EUKARYOTA; POTATO VIRUS M;

EID: 0034045453     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/16.4.313     Document Type: Article

References (54)

1. Aaronson, J.S., Eckman, B., Blevins, R.A., Borkowski, J.A., Myerson, J., Imran, S. and Elliston, K.O. (1996) Toward the development of a gene index to the human genome: an assessment of the nature of high-throughput EST sequence data. Genome Res., 6, 829-845.
2. Adams, et al. (1995) Initial assessment of human gene diversity and expression patterns based upon 83 million nucleotides of cDNA sequence. Nature, 377, Supplement 3, 174.
3. Altschul, S.F. and Erickson, B.W. (1986) Optimal sequence alignments using affine gap costs. Bull. Math. Biol., 48, 603-616.
4. Altschul, S.F., Madden, T.L., Schaffer, 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. Nucl. Acids Res., 25, 3389-3402.
5. Bailey, L.C., Searls, D.B. and Overton, G.C. (1998) Analysis of EST-driven gene annotation in human genomic sequence. Genome Res., 8, 362-376.
6. Battey, J., Jordan, E., Cox, D. and Dove, W. (1999) An action plan for mouse genomics. Nature Gen., 21, 73-75.
7. 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 Gen., 13, 167-174.
8. Benson, D.A., Boguski, M.S., Lipman, D.J., Ostell, J. and Ouellette, B.F.F. (1998) GenBank. Nucl. Acids Res., 26, 1-7.
9. Bishop, M. and Thompson, E. (1984) Fast computer search for similar DNA sequences. Nucl. Acids Res., 12, 5471-5474.
10. Blake, J.A., Eppig, J.T., Richardson, J.E., Davisson, M.T. and the Mouse Genome Informatics Group (1998) The Mouse Genome Database (MGD): a community resource. Status and enhancements. Nucl. Acids Res., 26, 130-137.
11. Boguski, M. and Schuler, G. (1995) Establishing a human transcript map. Nature Gen., 10, 369-371.
12. Boguski, M., Lowe, T.M.J. and Tolstoshev, C.M. (1993) dbEST - database for 'Expressed Sequence Tags'. Nature Gen., 4, 332.
13. Bonaldo, M.F., Lennon, G. and Soares, M.B. (1996) Normalization and subtraction: two approaches to facilitate gene discovery. Genome Res., 8, 791-806.
14. Bonfield J.K., Smith, K.F. and Staden, R. (1995) A new DNA sequence assembly program. Nucl. Acids Res., 24, 4992-4999.
15. Burke, J., Wang, H., Hide, W. and Davison, D.B. (1998) Alternative gene form discovery and candidate gene selection from gene indexing projects. Genome Res., 8, 276-290.
16. Chou, A. and Burke, J. (1999) CRAWview: for viewing splicing variation, gene families, and polymorphism in clusters of ESTs and full-length sequences. Bioinformatics, 15, 376-381.
17. Davidson, D., Bard, J., Brune, R., Burger, A., Dubreuil, C., Hill, W., Kaufman, M., Quinn, J. and Baldock, R. (1997) The mouse atlas and graphical gene-expression database. Cell Develop. Biol., 8, 509-517.
18. Eckman, B.A., Aaronson, J.S., Borkowski, J.A., Bailey, W.J., Elliston, K.O., Williamson, A.R. and Blevins, R.A. (1998) The Merck Gene Index browser: an extensible data integration system for gene finding, gene characterization and EST data mining. Bioinformatics, 14, 2-13.
19. Gautheret, D., Poirot, O., Lopez, F., Audic, S. and Claverie, J. (1998) Alternate polyadenylation in human mRNAs: A large-scale analysis by EST clustering. Genome Res., 8, 524-530.
20. Gerhold, D. and Caskey, T. (1996) Its the genes! EST access to human genome content. BioEssays, 18, 973-981.
21. Gill, R.W., Hodgman, T.C., Littler, C.B., Oxer, M.D., Montgomery, D.S., Taylor, S. and Sanseau, P. (1997) A new dynamic tool to perform assembly of expressed sequence tags (ESTs). Comput. Applic. Biosci., 13, 453-457.
22. Graul, R.C. and Sadée, W. (1997) Evolutionary relationships among proteins probed by an iterative neighborhood cluster analysis (INCA). Alignment of bacteriorhodopsins with the yeast sequence YRO2. Pharm. Res., 14, 1533-1541.
23. Grillo, G., Attimonelli, M., Liuni, S. and Pesole, G. (1996) Cleanup: a fast computer program for removing redundancies from nucleotide sequence datatbases. Comput. Applic. Biosci., 12, 1-8.
24. Hardison, R.C., Oeltjen, J. and Miller, W. (1997) Long human-mouse sequence alignments reveal novel regulatory elements: A reason to sequence the mouse genome. Genome Res., 7, 959-966.
25. Hide, W., Burke, J. and Davison, D.B. (1994) Biological evaluation of d2, an algorithm for high-performance sequence comparison. J. Comput. Biol., 1, 199-215.
26. Hillier, L., Lennon, G., Becker, M. Bonaldo, M.F. et al. (1996) Generation and analysis of 280000 human expressed sequence tags. Genome Res., 6, 807-828.
27. Houlgatte, R., Mariage-Samson, R., Duprat, S., Tessier, A., Bentolila, S., Lamy, B. and Auffray, C. (1995) The Genexpress Index: A resource for gene discovery and the genic map of the human genome. Genome Res., 5, 272-304.
28. Hu, J., Mungall, C., Nicholson, D. and Archibald, A.L. (1998) Design and implementation of a CORBA-based genome mapping system prototype. Bioinformatics, 14, 112-120.
29. Huang, X. (1996) An improved sequence assembly program. Genomics, 33, 21-31.
30. Jungfer, K. and Rodriguez-Tomé, P. (1998) Mapplet: a CORBA-based genome map viewer. Bioinformatics, 14, 734-738.
31. Jiang, J. and Jacob, H.J. (1998) EbEST: An automated tool using expressed sequence tags to delineate gene structure. Genome Res., 8, 268-275.
32. Lijnzaad, P., Helgesen, C. and Rodriguez-Tomé, P. (1998) The radiation hybrid database. Nucl. Acids Res., 26, 102-105.
33. Küster, B. and Mann, M. (1998) Identifying proteins and posttranslational modifications by mass sprectrometry. Curr. Opin. Struct. Biol., 8, 393-400.
34. Lopez, A.J. (1998) Alternative splicing of pre-mRNA: Developmental consequences and mechanisms of regulation. Annu. Rev. Genetic., 32, 279-305.
35. McCarthy, L.C., Terret, J., Davis, M.E., Knights, C.J., Smith, A.L., Critcher, R., Schmitt, K., Hudson, J., Spurr, N.K. and Goodfellow, P.N. (1997) A first-generation whole genome-radiation hybrid map spanning the mouse genome. Genome Res., 7, 1153-1161.
36. Makalowski, W., Zhang, J. and Boguski, M.S. (1996) Comparative analysis of 1196 orthologous mouse and human full-length mRNA and protein sequences. Genome Res., 6, 846-857.
37. Marra, M., Hillier, L. Kucaba, T. et al. (1999) An encyclopedia of mouse genes. Nature Gen., 21, 191-199.
38. Meyers, E.W. (1995) Toward simplifying and accurately formulating fragment assembly. J. Comput. Biol., 2, 275-290.
39. Miller, M.J. and Powell, J.I. (1994) A quantitative comparison of DNA sequence assembly programs. J. Comput. Biol., 4, 257-269.
40. Miller, C., Gurd, J. and Brass, A. (1999) A RAPID algorithm for sequence database comparisons: application to the identification of vector contamination in the EMBL databases. Bioinformatics, 15, 111-121.
41. Oliver, S.G. (1996) From DNA sequence to biological function. Nature, 379, 597-600.
42. Orfali, R. and Harkey, D. (1997) Client/Server Programming with JAVA and CORBA. Wiley, New York.
43. Orfali, R. and Harkey, D. (1998) Client/Server Programming with JAVA and CORBA. 2nd edn, Wiley, New York.
44. Parsons, J.D. (1995) Improved tools for DNA comparison and clustering. Comput. Applic. Biosci., 11, 603-613.
45. Parsons, J.D., Brenner, S. and Bishop, M.J. (1992) Clustering cDNA sequences. Comput. Applic. Biosci., 8, 461-466.
46. Parsons, J.D., Buehler, E. and Hillier, L. (1999) DNA sequence chromatogram browsing using JAVA and CORBA. Genome Res., 9, 277-281.
47. Pearson, W.R., Wood, T., Zhang, Z. and Miller, W. (1997) Comparison of DNA sequences with protein sequences. Genomics, 46, 24-36.
48. Rounsley, S.D., Glodek, A., Sutton, G., Adams, M.D., Somerville, C.R., Venter, J.C. and Kerlavage, A.R. (1996) The construction of Arabidopsis expressed sequence tag assemblies - A new resource to facilitate gene identification. Plant Pysiol., 112, 1177-1183.
49. Schuler et al. (1996) A gene map of the human genome. Science, 274, 540-546.
50. Stein, L.D. and Thierry-Mieg, J. (1998) Scriptable access to the Caenorhabditis elegans genome sequence and other ACEDB databases. Genome Res., 8, 1308-1315.
51. Stoesser, G., Moseley, M.A., Sleep, J., McGowran, M., Garcia-Pastor, M. and Sterk, P. (1998) The EMBL nucleotide sequence database. Nucl. Acids Res., 26, 8-15.
52. Sutton, G., White, O., Adams, M. and Kerlavage, A. (1995) TIGR assembler: A new tool for assembling large shotgun sequencing projects. Genome Sci. Technol., 1, 9-19.
53. Wolfsberg, T.G. and Landsman, D. (1997) A comparison of expressed sequence tags (ESTs) to human genomic sequences. Nucl. Acids Res., 25, 1626-1632.
54. Yee, D.P. and Conklin, D. (1998) Automated clustering and assembly of large EST collections., In Glasgow, J., Littlejohn, T., Lathrop, F.M.R., Sankoff, D. and Sensen, C. (eds), Proceedings ISMB-98. AAAI Press, pp. 203-211.