Nematode.net update 2008: Improvements enabling more efficient data mining and comparative nematode genomics

Nucleic Acids Research

Volumn 37, Issue SUPPL. 1, 2009, Pages

  Martin, John ^a   Abubucker, Sahar ^a   Wylie, Todd ^a   Yin, Yong ^a   Wang, Zhengyuan ^a   Mitreva, Makedonka ^a  

^a WASHINGTON UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ACCESS TO INFORMATION; ARTICLE; BIOINFORMATICS; CAENORHABDITIS ELEGANS; CODON USAGE; COMPUTER INTERFACE; COMPUTER PROGRAM; DATA MINING; DNA MICROARRAY; EXPRESSED SEQUENCE TAG; GENE EXPRESSION; INFORMATION DISSEMINATION; INFORMATION PROCESSING; INFORMATION RETRIEVAL; MICROBIAL GENETICS; NEMATODE; NONHUMAN; PRIORITY JOURNAL; PROTEIN DATABASE; PROTEIN FAMILY; SEQUENCE HOMOLOGY; WEB BROWSER;

ANIMALS; DATABASES, GENETIC; GENE EXPRESSION; GENOME, HELMINTH; GENOMICS; HELMINTH PROTEINS; NEMATODA;

ANIMALIA; CAENORHABDITIS ELEGANS; NEMATODA;

EID: 58149191260     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkn744     Document Type: Article

References (42)

1. WHO (2005) Deworming for health and development. Report of the third global meeting of the partners for parasite control. World Health Organization.
2. Bethony,J., Brooker,S., Albonico,M., Geiger,S.M., Loukas,A., Diemert,D. and Hotez,P.J. (2006) Soil-transmitted helminth infections: Ascariasis, trichuriasis, and hookworm. Lancet, 367, 1521-1532.
3. Chan,M.S. (1997) The global burden of intestinal nematode infections - fifty years on. Parasitol. Today, 13, 438-443.
4. Jasmer,D.P., Groverse,A. and Smant,G. (2003) Parasitic nematode interactions with mammals and plants. Annu. Rev. Phytopathol., 41, 245-270.
5. Wylie,T., Martin,J., Dante,M., Mitreva,M., Clifton,S.W., Chinwalla,A., Waterston,R.H., Wilson,R.K. and McCarter,J.P. (2004) Nematode.net: A tool for navigating sequences from parasitic and free-living nematodes. Nucleic Acids Res., 32, D423-D426.
6. Stein,L.D., Mungall,C., Shu,S., Caudy,M., Mangone,M., Day,A., Nickerson,E., Stajich,J.E., Harris,T.W., Arva,A. et al. (2002) The generic genome browser: A building block for a model organism system database. Genome Res., 12, 1599-1610.
7. Rogers,A., Antoshechkin,I., Bieri,T., Blasiar,D., Bastiani,C., Canaran,P., Chan,J., Chen,W.J., Davis,P., Fernandes,J. et al. (2008) WormBase 2007. Nucleic Acids Res., 36, D612-D617.
8. Gish,W. (1996-2002) http://blast.wustl.edu.
9. Blaxter,M.L., De Ley,P., Garey,J.R., Liu,L.X., Scheldeman,P., Vierstraete,A., Vanfleteren,J.R., Mackey,L.Y., Dorris,M., Frisse,L.M. et al. (1998) A molecular evolutionary framework for the phylum Nematoda. Nature, 392, 71-75.
10. Kanehisa,M. and Goto,S. (2006) KEGG: Kyoto encyclopedia of genes and genomes. Nucleic Acids Res., 28, 27-30.
11. IUBMB (1992) Enzyme Nomenclature: Recommendations of the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology. Academic Press, San Diego.
12. Moriya,Y., Itoh,M., Okuda,S., Yoshizawa,A.C. and Kanehisa,M. (2007) KAAS: An automatic genome annotation and pathway reconstruction server. Nucleic Acids Res., 35, W182-W185.
13. Ghedin,E., Wang,S., Spiro,D., Caler,E., Zhao,Q., Crabtree,J., Allen,J.E., Delcher,A.L., Guiliano,D.B., Miranda-Saavedra,D. et al. (2007) Draft genome of the filarial nematode parasite. Brugia malayi. Science, 317, 1756-1760.
14. Mitreva,M., Zarlenga,D.S., McCarter,J.P. and Jasmer,D.P. (2007) Parasitic nematodes-from genomes to control. Vet. Parasitol., 148, 31-42.
15. Bateman,A., Coin,L., Durbin,R., Finn,R.D., Hollich,V., Griffiths-Jones,S., Khanna,A., Marshall,M., Moxon,S., Sonnhammer,E.L. et al. (2004) The Pfam protein families database. Nucleic Acids Res. 32, D138-D141.
16. Stein,L.D., Bao,Z., Blasiar,D., Blumenthal,T., Brent,M.R., Chen,N., Chinwalla,A., Clarke,L., Clee,C., Coghlan,A. et al. (2003) The genome sequence of Caenorhabditis briggsae: A platform for comparative genomics. PLoS Biol., 1, E45.
17. Parkinson,J., Mitreva,M., Whitton,C., Thomson,M., Daub,J., Martin,J., Hall,N., Barrell,B., Waterston,R.H., McCarter,J.P. et al. (2004) A transcriptomic analysis of the phylum Nematoda. Nat. Genet., 36 1259-1267.
18. Panhuis,T.M., Clark,N.L. and Swanson,W.J. (2006) Rapid evolution of reproductive proteins in abalone and Drosophila. Philos. Trans. R Soc. Lond. B Biol. Sci., 361, 261-268.
19. Peng,J. and Huang,C.H. (2006) Rh proteins vs Amt proteins: An organismal and phylogenetic perspective on CO2 and NH3 gas channels. Transfus. Clin. Biol., 13, 85-94.
20. Givnish,T.J., Evans,T.M., Zjhra,M.L., Patterson,T.B., Berry,P.E. and Sytsma,K.J. (2000) Molecular evolution, adaptive radiation, and geographic diversification in the amphiatlantic family Rapateaceae: evidence from ndhF sequences and morphology. Int. J. Org. Evol., 54, 1915-1937.
21. Kocher,T.D. (2004) Adaptive evolution and explosive speciation: The cichlid fish model. Nat. Rev. Genet., 5, 288-298.
22. Jang,C.S., Jung,J.H., Yim,W.C., Lee,B.M., Seo,Y.W. and Kim,W. (2007) Divergence of genes encoding non-specific lipid transfer proteins in the poaceae family. Mol. Cells, 24, 215-223.
23. Lilley,C.J., Urwin,P.E. and Atkinson,H.J. (1999) Characterization of plant nematode genes: Identifying targets for a transgenic defence. Parasitology, 118, S63-S72.
24. Davis,E.L., Hussey,R.S. and Baum,T.J. (2004) Getting to the roots of parasitism by nematodes. Trends Parasitol., 20, 134-141.
25. Curtis,R.H.C. (2007) Plant parasitic nematode proteins and the host parasite interaction. Brief. Funct. Genomic Proteomic., 6, 50-58.
26. McCarter,J.P. (2004) Genomic filtering: An approach to discovering novel antiparasitics. Trends Parasitol., 20, 462-468.
27. Finn,R.D., Tate,J., Mistry,J., Coggill,P.C., Sammut,S.J., Hotz,H.-R., Ceric,G., Forslund,K., Eddy,S.R., Sonnhammer,E.L.L. et al. (2008) The Pfam protein families database. Nucleic Acids Res., 36, D281-D288.
28. Wasmuth,J.D. and Blaxter,M.L. (2004) prot4EST: Translating expressed sequence tags from neglected genomes. BMC Bioinformatics, 5, 187.
29. McCarter,J., Dautova Mitreva,M., Martin,J., Dante,M., Wylie,T., Rao,U., Pape,D., Bowers,Y., Theising,B., Murphy,C.V. et al. (2003) Analysis and Functional Classi.cation of Transcripts from the Nematode Meloidogyne incognita. Genome Biol., 4, R26.
30. Mitreva,M., McCarter,J.P., Martin,J., Dante,M., Wylie,T., Chiapelli,B., Pape,D., Clifton,S.W., Nutman,T.B. and Waterston,R.H. (2004) Comparative genomics of gene expression in the parasitic and free-living nematodes Strongyloides stercoralis and Caenorhabditis elegans. Genome Res., 14, 209-220.
31. Enright,A.J., Van Dongen,S. and Ouzounis,C.A. (2002) An efficient algorithm for large-scale detection of protein families. Nucleic Acids Res., 30, 1575-1584.
32. Wasmuth,J., Schmid,R., Hedley,A. and Blaxter,M. (2008) On the extent and origins of genic novelty in the phylum nematoda. PloS Negl. Trop. Dis., 2, e258.
33. Parkinson,J., Whitton,C., Schmid,R., Thomson,M. and Blaxter,M. (2004) NEMBASE: A resource for parasitic nematode ESTs. Nucleic Acids Res. 32, D427-D430.
34. Kall,L., Krogh,A. and Sonnhammer,E.L.L. (2004) A combined transmembrane topology and signal peptide prediction method. J. Mol. Biol., 338, 1027-1036.
35. Gewehr,J.E. and Zimmer,R. (2006) SSEP-Domain: Protein domain prediction by alignment of secondary structure elements and profiles. Bioinformatics, 22, 181-187.
36. McGuffin,L.J., Bryson,K. and Jones,D.T. (2000) The PSIPRED protein structure prediction server. Bioinformatics, 16, 404-405.
37. Ward,J.J., McGuffin,L.J., Bryson,K., Buxton,B.F. and Jones,D.T. (2004) The DISOPRED server for the prediction of protein disorder. Bioinformatics, 20, 2138-2139.
38. Yin,Y., Martin,J., Abubucker,S., Scott,A.L., McCarter,J.P., Wilson,R.K., Jasmer,D.P. and Mitreva,M. (2008) Intestinal transcriptomes of nematodes: Comparison of the parasites Ascaris suum and Haemonchus contortus with the free-living Caenorhabditis elegans. PLoS Negl. Trop. Dis., 2, e269.
39. Elling,A., Mitreva,M., Recknor,J., Gai,X., Martin,J., Maier,T., McDermott,J., Hewezi,T., McK Bird,D., Davis,E. et al. (2007) Divergent evolution of arrested development in the dauer stage of Caenorhabditis elegans and the infective stage of Heterodera glycines. Genome Biol., 8, R211.
40. Abubucker,S., Martin,J., Yin,Y., Fulton,L., Yang,S.-P., Hallsworth-Pepin,K., Johnston,J.S., Hawdon,J., McCarter,J.P., Wilson,R.K. et al. (2008) The canine hookworm genome: Analysis and classiffication of Ancylostoma caninum survey sequences. Mol. Biochem. Parasitol., 157, 187-192.
41. Cantarel,B.L., Korf,I., Robb,S.M.C., Parra,G., Ross,E., Moore,B., Holt,C., Sanchez Alvarado,A. and Yandell,M. (2008) MAKER: An easy-to-use annotation pipeline designed for emerging model organism genomes. Genome Res., 18, 188-196.
42. Birney,E., Clamp,M. and Durbin,R. (2004) GeneWise and Genomewise. Genome Res., 14, 988-995.