EST clustering error evaluation and correction

Bioinformatics

Volumn 20, Issue 17, 2004, Pages 2973-2984

  Wang, Ji Ping Z ^a,b   Lindsay, Bruce G ^b   Leebens Mack, James ^b   Cui, Liying ^b   Wall, Kerr ^b   Miller, Webb C ^b   dePamphilis, Claude W ^b  

^a NORTHWESTERN UNIVERSITY   (United States)

^b PENNSYLVANIA STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

COMPLEMENTARY DNA;

ACCURACY; ANALYTICAL ERROR; ARABIDOPSIS; ARTICLE; CLUSTER ANALYSIS; COMPUTER PROGRAM; CONTROLLED STUDY; DNA LIBRARY; EXPRESSED SEQUENCE TAG; GENE CLUSTER; GENE EXPRESSION; GENE EXPRESSION PROFILING; GENETIC ANALYSIS; NONHUMAN; PRIORITY JOURNAL; QUANTITATIVE ANALYSIS;

EID: 10244224129     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/bth342     Document Type: Article

References (31)

1. Adams,M.D., Kerlavage,A.R., Fields,C. and Venter,J.C. (1993) 3,400 new expressed sequence tags identify diversity of transcripts in human brain. Nat. Genet., 4, 256-267.
2. Adams,M.D., Dubnick,M., Kerlavage,A.R., Moreno,R., Kelley,J.M., Utterback,T.R., Nagle,J.W., Fields,C. and Venter,J.C. (1992) Sequence identification of 2,375 human brain genes. Nature, 355 632-634.
3. Asamizu,E., Nakamura,Y., Sato,S. and Tabata,S. (2000) A large scale analysis of cDNA in Arabidopsis thaliana: generation of 12,028 non-redundant expressed sequence tags from normalized and size-selected cDNA libraries. DNA Res., 7, 175-180.
4. Audic,S. and Claverie,J.M. (1997) Computational methods for the identification of differential and coordinated gene expression. Human Mol. Genet., 8, 1821-1832.
5. Boguski,M.S. and Schuler,G.D. (1995) ESTablishing a human transcript map. Nat. Genet., 10, 369-371.
6. Burke,J., Davison,D. and Hide,W. (1999) d2_cluster: a validated method for clustering EST and full-length cDNA sequences. Genome Res., 9, 1135-1142.
7. Burke,J., Wang,H., Hide,W. and Davison,D. (1998) Alternative gene form discovery and candidate gene selection from gene indexing projects. Genome Res., 8, 276-290.
8. 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.
9. Christoffels,A., Van Gelder,A., Greyling,G., Miller,R., Hide,J. and Hide,W. (2001) STACK: Sequence Tag Alignment and Consensus Knowledgebase. Nucleic Acids Res., 29, 234-238.
10. Duret,L. and Mouchiroud,D. (1999) Expression pattern and, surprisingly, gene length shape codon usage in Caenorhabditis, Drosophila, and Arabidopsis. Proc. Nat. Acad. Sci., USA, 96 4482-4487.
11. Green,P. (1996) Phrap. documentation. University of Washington, Seattle.
12. Haas,B.J., Volfovsky,N., Town,C.D., Troukhan,M., Alexandrov,N., Feldmann,K.A., Flavell,R.B., White,O. and Salzberg,S.L. (2002) Full-length messenger RNA sequences greatly improve genome annotation. Genome Biol., 3, Epub 2002 May 30.
13. Harrison,P.M., Kumar,A., Lang,N., Snyder,M. and Gerstein,M. (2002) A question of size: the eukaryotic proteome and the problems in defining it. Nucleic Acids Res., 30, 1083-1090.
14. Heber,S., Alekseyev,M., Sze,S.H., Tang,H. and Pevzner,P.A. (2002) Splicing graphs and EST assembly problem. Bioinformatics, 18, 181-188.
15. Hu,G., Modrek,B., Stensland,R.H.M., Saarela,J., Pajukanta,P., Kustanovich,V., Peltonen,L., Nelson,S.F. and Lee,C. (2002) Efficient discovery of single-nucleotide polymorphisms in coding regions of human genes. Pharmacogenomics J., 2, 236-242.
16. Huang,X. and Madan,A. (1999) CAP3: a DNA sequence assembly program. Genome Res., 6, 829-845.
17. Khan,A.S., Wileox,A.S., Polymeropoulos,M.H., Hopkins,J.A., Stevens,T.J., Robinson,M.R., Orpana,A.k. and Sikela,J.M. (1992) Single pass sequencing and physical and genetic mapping of human brain cDNAs. Nat. Genet., 2, 180-185.
18. Lee,C. (2003) Generating consensus sequences from partial order multiple sequence alignment graphs. Bioinformatics, 19, 999-1008.
19. Liang,F., Holt,I., Pertea,G., Karamycheva,S., Salzberg,S.L. and Quackenbush,J. (2000) An optimized protocol for analysis of EST sequences. Nucleic Acids Res., 28, 3657-3665.
20. Miller,R.T., Christoffels,A.G., Gopalakrishnan,C., Burke,J., Ptitsyn,A.A., Broveak,T.R. and Hide,W.A. (1999) A comprehensive approach to clustering of expressed human gene sequence: the sequence tag alignment and consensus knowledge base. Genome Res., 9, 1143-1155.
21. Modrek,B. and Lee,C. (2002) A genomic view of alternative splicing. Nat. Genet., 30, 13-19.
22. Modrek,B., Resch,A., Grasso,C. and Lee,C. (2001) Genome-wide detection of alternative splicing in expressed sequences of human genes. Nucleic Acids Res., 29, 2850-2859.
23. Picoult-Newberg,L., Ideker,T.E., Pohl,M.G., Taylor,S.L., Donaldson,M.A., Nickerson,D.A. and Boyce-Jacino,M. (1999) Mining SNPs from EST databases. Genome Res., 9, 167-174.
24. Schuler,G.D., Boquski,M.S., Stewart,E.A., Stein,L.D., Gyapay,G., Rice,K., White,R.E., Rodriquez-Tome,P., Aggarwal,A., Bajorek,E. et al. (1996) A gene map of the human genome. Science 274, 540-546.
25. Seki,M., Narusaka,M., Kamiya,A., Ishida,J., Satou,M., Sakurai,T., Nakajima,M., Enju,A., Akiyama,K., Oono,Y. et al. (2002) Functional annotation of a full-length Arabidopsis cDNA collection. Science, 296, 141-145.
26. Stekel,D.J., Git,Y. and Falciani,F. (2000) The comparison of gene expression from multiple cDNA libraries. Genome Res., 10 2055-2061.
27. Sutton,G., White,O., Adams,M.D. and Kerlavage,A.R. (1995) TIGR assembler: a new tool for assembling large shotgun sequencing projects. Genome Sci. Technol., 1, 9-18.
28. The Arabidopsis Genome Initiative (2000) Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature, 408, 796-815.
29. Van der Hoeven,R., Ronning,C., Giovannoni,J., Martin,G. and Tanksley,S. (2002) Deductions about the number, organization, and evolution of genes in the tomato genome based on analysis of a large expressed sequence tag collection and selective genomic sequencing. Plant Cell, 14, 1441-1456.
30. Wright,F.A., Lemon,W.J., Zhao,W.D, Sears,R., Zhuo,D., Wang,J.P., Yang,H.Y., Baer,T., Stredney,D., Spitzner,J. et al. (2001) A draft annotation and overview of the human genome. Genome Biol., 2, 1-18.
31. Xu,Q., Modrek,B. and Lee,C. (2002) Genome-wide detection of tissue-specific alternative splicing in the human transcriptome. Nucleic Acids Res., 30, 3754-3766.