MEGANTE: A web-based system for integrated plant genome annotation

Plant and Cell Physiology

Volumn 55, Issue 1, 2014, Pages

  Numa, Hisataka ^a   Itoh, Takeshi ^a  

^a NATIONAL INSTITUTE OF AGROBIOLOGICAL SCIENCES   (Japan)

Author keywords

Gene prediction; Plant genome annotation; Web service

Indexed keywords

ARTICLE; COMPUTER INTERFACE; GENE PREDICTION; GENETIC DATABASE; GENETICS; INTERNET; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PLANT GENE; PLANT GENOME; PLANT GENOME ANNOTATION; WEB SERVICE;

GENE PREDICTION; PLANT GENOME ANNOTATION; WEB SERVICE;

BASE SEQUENCE; DATABASES, GENETIC; GENES, PLANT; GENOME, PLANT; INTERNET; MOLECULAR SEQUENCE ANNOTATION; USER-COMPUTER INTERFACE;

EID: 84892684968     PISSN: 00320781     EISSN: 14719053     Source Type: Journal    
DOI: 10.1093/pcp/pct157     Document Type: Article

References (45)

1. Allen, J.E., Majoros, W.H., Pertea, M. and Salzberg, S.L. (2006) JIGSAW, GeneZilla, and GlimmerHMM: puzzling out the features of human genes in the ENCODE regions. Genome Biol. 7(Suppl. 1), S9.1-S9.13.
2. Amano, N., Tanaka, T., Numa, H., Sakai, H. and Itoh, T. (2010) Efficient plant gene identification based on interspecies mapping of full-length cDNAs. DNA Res. 17: 271-279.
3. Ashburner, M., Ball, C.A., Blake, J.A., Botstein, D., Butler, H., Cherry, J.M. et al. (2000) Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat. Genet. 25: 25-29.
4. Bevan, M.W. and Uauy, C. (2013) Genomics reveals new landscapes for crop improvement. Genome Biol. 14: 206.
5. Bombarely, A., Menda, N., Tecle, I.Y., Buels, R.M., Strickler, S., Fischer-York, T. et al. (2011) The Sol Genomics Network (solgen-omics.net): growing tomatoes using Perl. Nucleic Acids Res. 39: D1149-D1155.
6. Camacho, C., Coulouris, G., Avagyan, V., Ma, N., Papadopoulos, J., Bealer, K. et al. (2009) BLAST+: architecture and applications. BMC Bioinformatics 10: 421.
7. Cantarel, B.L., Korf, I., Robb, S.M., Parra, G., Ross, E., Moore, B. et al. (2008) MAKER: an easy-to-use annotation pipeline designed for emerging model organism genomes. Genome Res. 18: 188-196.
8. Chen, T., Zhang, Y., Zhao, L., Zhu, Z., Lin, J., Zhang, S. et al. (2009) Fine mapping and candidate gene analysis of a green-revertible albino gene gra(t) in rice. J. Genet. Genomics 36: 117-123.
9. Choulet, F., Wicker, T., Rustenholz, C., Paux, E., Salse, J., Leroy, P. et al. (2010) Megabase level sequencing reveals contrasted organization and evolution patterns of the wheat gene and transposable element spaces. Plant Cell 22: 1686-1701.
10. Cooper, L., Walls, R.L., Elser, J., Gandolfo, M.A., Stevenson, D.W., Smith, B. et al. (2013) The plant ontology as a tool for comparative plant anatomy and genomic analyses. Plant Cell Physiol. 54: e1.
11. Droc, G., Larivière, D., Guignon, V., Yahiaoui, N., This, D., Garsmeur, O. et al. (2013) The banana genome hub. Database (Oxford) 2013: bat035.
12. Duvick, J., Fu, A., Muppirala, U., Sabharwal, M., Wilkerson, M.D., Lawrence, C.J. et al. (2008) PlantGDB: a resource for comparative plant genomics. Nucleic Acids Res. 36: D959-D965.
13. Goff, S.A., Vaughn, M., McKay, S., Lyons, E., Stapleton, A.E., Gessler, D. et al. (2011) The iPlant Collaborative: cyberinfrastructure for plant biology. Front. Plant Sci. 2: 34.
14. Goodstein, D.M., Shu, S., Howson, R., Neupane, R., Hayes, R.D., Fazo, J. et al. (2012) Phytozome: a comparative platform for green plant genomics. Nucleic Acids Res. 40: D1178-D1186.
15. Haas, B.J., Delcher, A.L., Mount, S.M., Wortman, J.R., Smith, R.K., Hannick, L.I. et al. (2003) Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies. Nucleic Acids Res. 31: 5654-5666.
16. Hunter, S., Jones, P., Mitchell, A., Apweiler, R., Attwood, T.K., Bateman, A. et al. (2012) InterPro in 2011: new developments in the family and domain prediction database. Nucleic Acids Res. 40: D306-D312.
17. Jaillon, O., Aury, J.M., Noel, B., Policriti, A., Clepet, C., Casagrande, A. et al. (2007) The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla. Nature 449: 463-467.
18. Jung, S., Staton, M., Lee, T., Blenda, A., Svancara, R., Abbott, A. et al. (2008) GDR (Genome Database for Rosaceae): integrated web-database for Rosaceae genomics and genetics data. Nucleic Acids Res. 36: D1034-D1040.
19. Kent, W.J. (2002) BLAT-the BLAST-like alignment tool. Genome Res. 12: 656-664.
20. Korf, I. (2004) Gene finding in novel genomes. BMC Bioinformatics 5
21. Lamesch, P., Berardini, T.Z., Li, D., Swarbreck, D., Wilks, C., Sasidharan, R. et al. (2012) The Arabidopsis Information Resource (TAIR): improved gene annotation and new tools. Nucleic Acids Res. D1202-D1210.
22. Leroy, P., Guilhot, N., Sakai, H., Bernard, A., Choulet, F., Theil, S. et al. (2012) TriAnnot: a versatile and high performance pipeline for the automated annotation of plant genomes. Front. Plant Sci. 3: 5.
23. Lukashin, A.V. and Borodovsky, M. (1998) GeneMark.hmm: new solutions for gene finding. Nucleic Acids Res. 26: 1107-1115.
24. Magrane, M. and UniProt Consortium (2011) UniProt Knowledgebase: a hub of integrated protein data. Database (Oxford) 2011: bar009.
25. Majoros, W.H. and Salzberg, S.L. (2004) An empirical analysis of training protocols for probabilistic gene finders. BMC Bioinformatics 5: 206.
26. Mihara, M., Itoh, T. and Izawa, T. (2010) SALAD database: a motif-based database of protein annotations for plant comparative gen-omics. Nucleic Acids Res. 38: D835-D842.
27. Nagamura, Y., Antonio, B.A., Sato, Y., Miyao, A., Namiki, N., Yonemaru, J. et al. (2011) Rice TOGO Browser: a platform to retrieve integrated information on rice functional and applied genomics. Plant Cell Physiol. 52: 230-237.
28. Nakamura, Y., Cochrane, G., Karsch-Mizrachi, I. and The International Nucleotide Sequence Database Collaboration (2013) The International Nucleotide Sequence Database Collaboration. Nucleic Acids Res. 41: D21-D24.
29. Nussbaumer, T., Martis, M.M., Roessner, S.K., Pfeifer, M., Bader, K.C., Sharma, S. et al. (2013) MIPS PlantsDB: a database framework for comparative plant genome research. Nucleic Acids Res. 41: D1144-D1151.
30. Pavy, N., Rombauts, S., Déhais, P., Mathé, C., Ramana, D.V., Leroy, P. et al. (1999) Evaluation of gene prediction software using a genomic data set: application to Arabidopsis thaliana sequences. Bioinformatics 15: 887-899.
31. Podicheti, R., Gollapudi, R. and Dong, Q. (2009) WebGBrowse-a web server for GBrowse. Bioinformatics 25: 1550-1551.
32. Quevillon, E., Silventoinen, V., Pillai, S., Harte, N., Mulder, N., Apweiler, R. et al. (2005) InterProScan: protein domains identifier. Nucleic Acids Res. 33: W116-W120.
33. Rogic, S., Mackworth, A.K. and Ouellette, F.B. (2001) Evaluation of gene-finding programs on mammalian sequences. Genome Res. 11: 817-832.
34. Rouard, M., Guignon, V., Aluome, C., Laporte, M.A., Droc, G., Walde, C. et al. (2011) GreenPhylDB v2.0: comparative and functional genomics in plants. Nucleic Acids Res. 39: D1095-D1102.
35. Sakai, H., Lee, S.S., Tanaka, T., Numa, H., Kim, J., Kawahara, Y. et al. (2013) Rice Annotation Project Database (RAP-DB): an integrative and interactive database for rice genomics. Plant Cell Physiol. 54: e6.
36. Sakata, K., Nagamura, Y., Numa, H., Antonio, B.A., Nagasaki, H., Idonuma, A. et al. (2002) RiceGAAS: an automated annotation system and database for rice genome sequence. Nucleic Acids Res. 30: 98-102.
37. Salamov, A.A. and Solovyev, V.V. (2000) Ab initio gene finding in Drosophila genomic DNA. Genome Res. 10: 516-522.
38. Sayers, E.W., Barrett, T., Benson, D.A., Bolton, E., Bryant, S.H., Canese, K. et al. (2012) Database resources of the National Center for Biotechnology Information. Nucleic Acids Res. 40: D13-D25.
39. Stanke, M. and Waack, S. (2003) Gene prediction with a hidden Markov model and a new intron submodel. Bioinformatics 19(Suppl. 2), ii215-ii225.
40. Stein, L.D., Mungall, C., Shu, S., Caudy, M., Mangone, M., Day, A. et al. (2002) The generic genome browser: a building block for a model organism system database. Genome Res. 12: 1599-1610.
41. Walenz, B. and Florea, L. (2011) Sim4db and Leaff: utilities for fast batch spliced alignment and sequence indexing. Bioinformatics 27: 1869-1870.
42. Xu, J., Wang, B., Wu, Y., Du, P., Wang, J., Wang, M. et al. (2011) Fine mapping and candidate gene analysis of ptgms2-1, the photoperiod-thermo- sensitive genic male sterile gene in rice (Oryza sativa L.). Theor. Appl. Genet. 122: 365-372.
43. Yandell, M. and Ence, D. (2012) A beginner's guide to eukaryotic genome annotation. Nat. Rev. Genet. 13: 329-342.
44. Yao, H., Guo, L., Fu, Y., Borsuk, L.A., Wen, T.J., Skibbe, D.S. et al. (2005) Evaluation of five ab initio gene prediction programs for the discovery of maize genes. Plant Mol. Biol. 57: 445-460.
45. Youens-Clark, K., Buckler, E., Casstevens, T., Chen, C., Declerck, G., Derwent, P. et al. (2011) Gramene database in 2010: updates and extensions. Nucleic Acids Res. 39: D1085-D1094.