SpringerProtocols: Abstract: 3. Parasite Genome Databases and Web-Based Resources

3. Parasite Genome Databases and Web-Based Resources

By: Christiane Hertz-Fowler², Neil Hall³

Abstract

Full Text

Download PDF (513K)

In the last decade, high-throughput genome sequencing and complementary techniques such as microarray and proteomics have generated, and will continue to generate, ever-increasing amounts of data. These technologies of gene discovery, expression, and functional analysis have been applied to a vast array of organisms, including parasites. In most instances, the data are freely available via the Internet, and researchers are becoming increasingly reliant on up-to-date, centralized data repositories to complement wet bench science.

This chapter presents an overview of resources relevant to researchers with an interest in parasite genomics and biology. After briefly touching on some of the publicly available nucleotide and protein sequence as well as domain databases, the focus turns to parasite genome projects and associated Web-based resources. A list of parasite sequencing projects current at the time of writing, including relevant Web site addresses, is provided. The available resources range from network sites and project pages at sequencing institutes to databases that integrate and curate sequence data and associated annotation with diverse biological datasets. Particular attention is given to three databases, GeneDB (http://www.genedb.org/), PlasmoDB (http://plasmodb.org/), and tigr db, detailing the scope of each database and the tools available for data querying and retrieval.

Affiliation(s): (2) Pathogen Sequencing Unit, Wellcom Trust Sanger Institute, Hinxton, Cambridgeshire, UK
(3) Informatics, The Institute for Genomic Research, Rockville, MD

Book Title: Parasite Genomics Protocols

Series: Methods in Molecular Biology | Volume: 270 | Pub. Date: May-17-2004 | Page Range: 45-74 | DOI: 10.1385/1-59259-793-9:045

Subject: Genetics/Genomics

Key Words: Annotation - data curation - genome databases - parasite sequencing projects - Web resource

References

Download References

1.	Gardner, M. J., Hall, N., Fung, E., et al. (2002) Genome sequence of the human malaria parasite Plasmodium falciparum. Nature 419, 498–511.

2.	Stoesser, G., Baker, W., Van Den Broek, A., et al. (2003) The EMBL Nucleotide Sequence Database: major new developments. Nucleic Acids Res. 31, 17–22.

3.	Benson, D. A., Karsch-Mizrachi, I., Lipman, D. J., et al. (2003) GenBank. Nucleic Acids Res. 31, 23–27.

4.	Miyazaki, S., Sugawara, H., Gojobori, T., et al. (2003) DNA Data Bank of Japan (DDBJ) in XML. Nucleic Acids Res. 31, 13–16.

5.	O’Donovan, C., Martin, M. J., Gattiker, A., et al. (2002) High-quality protein knowledge resource: SWISS-PROT and TrEMBL. Brief Bioinform 3, 275–284.

6.	Boeckmann, B., Bairoch, A., Apweiler, R., et al. (2003) The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003. Nucleic Acids Res. 31, 365–370.

7.	Mulder, N. J., Apweiler, R., Attwood, T. K., et al. (2003) The InterPro Database, 2003 brings increased coverage and new features. Nucleic Acids Res. 31, 315–318.

8.	Wheeler, D. L., Church, D. M., Federhen, S., et al. (2003) Database resources of the National Center for Biotechnology. Nucleic Acids Res. 31, 28–33.

9.	Brooksbank, C., Camon, E., Harris, M. A., et al. (2003) The European Bioinformatics Institute’s data resources. Nucleic Acids Res. 31, 43–50.

10.	Janssen, C. S., Barrett, M. P., Lawson, D., et al. (2001) Gene discovery in Plasmodium chabaudi by genome survey sequencing. Mol. Biochem. Parasitol. 113, 251–260.

11.	El-Sayed, N. M. and Donelson, J. E. (1997) A survey of the Trypanosoma brucei rhodesiense genome using shotgun sequencing. Mol. Biochem. Parasitol. 84, 167–178.

12.	Liu, C., Vigdorovich, V., Kapur, V., et al. (1999) A random survey of the Cryptosporidium parvum genome. Infect. Immun. 67, 3960–3969.

13.	Smith, M. W., Aley, S. B., Sogin, M., et al. (1998) Sequence survey of the Giardia lamblia genome. Mol. Biochem. Parasitol. 95, 267–280.

14.	Carlton, J. M., Angiuoli, S. V., Suh, B. B., et al. (2002) Genome sequence and comparative analysis of the model rodent malaria parasite Plasmodium yoelii yoelii. Nature 419, 512–519.

15.	Katinka, M. D., Duprat, S., Cornillot, E., et al. (2001) Genome sequence and gene compaction of the eukaryote parasite Encephalitozoon cuniculi. Nature 414, 450–453.

16.	McDonagh, P. D., Myler, P. J., and Stuart, K. (2000) The unusual gene organization of Leishmania major chromosome 1 may reflect novel transcription processes. Nucleic Acids Res. 28, 2800–2803.

17.	Worthey, E. A., Martinez-Calvillo, S., Schnaufer, A., et al. (2003) Leishmania chromosome 3 contains two long convergent polycistronic gene clusters separated by a tRNA gene. Nucleic Acids Res. 31, 4201–4210.

18.	Hall, N., Berriman, M., Lennard, N. J., et al. (2003) The DNA sequence of chromosome I of an African trypanosome: gene content, chromosome organisation, recombination and polymorphism. Nucleic Acids Res. 31, 4864–4873.

19.	El-Sayed, N. M., Ghedin, E., Song, J., et al. (2003) The sequence and analysis of Trypanosoma brucei chromosome II. Nucleic Acids Res. 31, 4856–4863.

20.	El-Sayed, N. M., Alarcon, C. M., Beck, J. C., et al. (1995) cDNA expressed sequence tags of Trypanosoma brucei rhodesiense provide new insights into the biology of the parasite. Mol. Biochem. Parasitol. 73, 75–90.

21.	Verdun, R. E., Di Paolo, N., Urmenyi, T. P., et al. (1998) Gene discovery through expressed sequence Tag sequencing in Trypanosoma cruzi. Infect. Immun. 66, 5393–5398.

22.	Blaxter, M., Daub, J., Guiliano, D., et al. (2002) The Brugia malayi genome project: expressed sequence tags and gene discovery. Trans. R. Soc. Trop. Med. Hyg. 96, 7–17.

23.	Parkinson, J., Whitton, C., Guiliano, D., et al. (2001) 200000 nematode expressed sequence tags on the Net. Trends Parasitol. 17, 394–396.

24.	Manger, I. D., Hehl, A., Parmley, S., et al. (1998) Expressed sequence tag analysis of the bradyzoite stage of Toxoplasma gondii: identification of developmentally regulated genes. Infect. Immun. 66, 1632–1637.

25.	McArthur, A. G., Morrison, H. G., Nixon, J. E., et al. (2000) The Giardia genome project database. FEMS Microbiol. Lett. 189, 271–273.

26.	Liang, F., Holt, I., Pertea, G., et al. (2000) An optimized protocol for analysis of EST sequences. Nucleic Acids Res. 28, 3657–3665.

27.	Parkinson, J., Mitreva, M., Hall, N., et al. (2003) 400000 nematode ESTs on the Net. Trends Parasitol. 19, 283–286.

28.	Hertz-Fowler, C. and Peacock, C. S. (2002) Introducing GeneDB: a generic database. Trends Parasitol. 18, 465–467.

29.	Rutherford, K., Parkhill, J., Crook, J., et al. (2000) Artemis: sequence visualization and annotation. Bioinformatics 16, 944–945.

30.	Clayton, C., Adams, M., Almeida, R., et al. (1998) Genetic nomenclature for Trypanosoma and Leishmania. Mol. Biochem. Parasitol. 97, 221–224.

31.	Kissinger, J. C., Brunk, B. P., Crabtree, J., et al. (2002) The Plasmodium genome database. Nature 419, 490–492.

32.	Bahl, A., Brunk, B., Crabtree, J., et al. (2003) PlasmoDB: the Plasmodium genome resource. A database integrating experimental and computational data. Nucleic Acids Res. 31, 212–215.

33.	Tarleton, R. L. and Kissinger, J. (2001) Parasite genomics: current status and future prospects. Curr. Opin. Immunol. 13, 395–402.

34.	Oliveira, G. and Johnston, D. A. (2001) Mining the schistosome DNA sequence database. Trends Parasitol. 17, 501–503.

35.	Roos, D. S., Crawford, M. J., Donald, R. G., et al. (2002) Mining the Plasmodium genome database to define organellar function: what does the apicoplast do? Philos. Trans. R. Soc. Lond. B. Biol. Sci. 357, 35–46.

36.	Stein, L. D., Mungall, C., Shu, S., et al. (2002) The generic genome browser: a building block for a model organism system database. Genome Res. 12, 1599–1610.

37.	Stein, L. D. (2002) Creating a bioinformatics nation. Nature 417, 119–120.

38.	Wu, C. H., Yeh, L. S., Huang, H., et al. (2003) The Protein Information Resource. Nucleic Acids Res. 31, 345–347.

39.	Bateman, A., Birney, E., Cerruti, L., et al. (2002) The Pfam protein families database. Nucleic Acids Res. 30, 276–280.

40.	Attwood, T. K., Bradley, P., Flower, D. R., et al. (2003) PRINTS and its automatic supplement, prePRINTS. Nucleic Acids Res. 31, 400–402.

41.	Servant, F., Bru, C., Carrere, S., et al. (2002) ProDom: automated clustering of homologous domains. Brief Bioinform. 3, 246–251.

42.	Sigrist, C. J., Cerutti, L., Hulo, N., et al. (2002) PROSITE: a documented database using patterns and profiles as motif descriptors. Brief Bioinform. 3, 265–274.

43.	Letunic, I., Goodstadt, L., Dickens, N. J., et al. (2002) Recent improvements to the SMART domain-based sequence annotation resource. Nucleic Acids Res. 30, 242–244.

44.	Haft, D. H., Selengut, J. D., and White, O. (2003) The TIGRFAMs database of protein families. Nucleic Acids Res. 31, 371–373.

45.	Myler, P. J., Beverley, S. M., Cruz, A. K., et al. (2001) The Leishmania genome project: new insights into gene organization and function. Med. Microbiol. Immunol. (Berl.) 190, 9–12.

46.	El-Sayed, N. M., Hegde, P., Quackenbush, J., et al. (2000) The African trypanosome genome. Int. J. Parasitol. 30, 329–345.

47.	Adam, R. D. (2000) The Giardia lamblia genome. Int. J. Parasitol. 30, 475–484.

48.	Spano, F. and Crisanti, A. (2000) Cryptosporidium parvum: the many secrets of a small genome. Int. J. Parasitol. 30, 553–565.

49.	Shirley, M. W. (2000) The genome of Eimeria spp., with special reference to Eimeria tenella—a coccidium from the chicken. Int. J. Parasitol. 30, 485–493.

50.	Carlton, J. M., Muller, R., Yowell, C. A., et al. (2001) Profiling the malaria genome: a gene survey of three species of malaria parasite with comparison to other apicomplexan species. Mol. Biochem. Parasitol. 118, 201–210.

51.	Nene, V., Bishop, R., Morzaria, S., et al. (2000) Theileria parva genomics reveals an atypical apicomplexan genome. Int. J. Parasitol. 30, 465–474.

52.	Kissinger, J. C., Gajria, B., Li, L., et al. (2003) ToxoDB: accessing the Toxoplasma gondii genome. Nucleic Acids Res. 31, 234–236.

53.	Blaxter, M., Aslett, M., Guiliano, D., et al. (1999) Parasitic helminth genomics. Filarial Genome Project. Parasitology 118(Suppl.), S39–S51.

54.	Williams, S. A. and Johnston, D. A. (1999) Helminth genome analysis: the current status of the filarial and schistosome genome projects. Filarial Genome Project. Schistosome Genome Project. Parasitology 118(Suppl.), S19–S38.

55.	Williams, S. A., Laney, S. J., Lizotte-Waniewski, M., et al. (2002) The River Blindness Genome Project. Trends Parasitol. 18, 86–90.

Comments (Loading...)

Post comment/View all comments