WeGAS: A web-based microbial genome annotation system

Bioscience, Biotechnology and Biochemistry

Volumn 73, Issue 1, 2009, Pages 213-216

  Lee, Daesang ^a,b,c   Seo, Hwajung ^b   Park, Chankyu ^a   Park, Kiejung ^b  

^a Korea Advanced Institute of Science and Technology (KAIST)   (South Korea)

^b SmallSoft Co Ltd   (South Korea)

^c Korea Bio Polytechnic   (South Korea)

Author keywords

Annotation; Computational analysis; Gene ontology; Genome; Homology

Indexed keywords

DATA VISUALIZATION; DATABASE SYSTEMS; OPTICAL PROJECTORS;

ANNOTATION; COMPUTATIONAL ANALYSIS; GENE ONTOLOGY; GENOME; HOMOLOGY;

ONTOLOGY;

ALGORITHM; ARTICLE; BACTERIAL GENE; BACTERIAL GENOME; COMPUTER GRAPHICS; GENETIC DATABASE; INFORMATION RETRIEVAL; INTERNET;

ALGORITHMS; COMPUTER GRAPHICS; DATABASES, GENETIC; GENES, BACTERIAL; GENOME, BACTERIAL; INFORMATION STORAGE AND RETRIEVAL; INTERNET;

EID: 58849134234     PISSN: 09168451     EISSN: 13476947     Source Type: Journal    
DOI: 10.1271/bbb.80567     Document Type: Article

References (15)

1. Sakiyama, T., Takami, H., Ogasawara, N., Kuhara, S., Kozuki, T., Doga, K., Ohyama, A., and Horikoshi, K., An automated system for genome analysis to support microbial whole-genome shotgun sequencing. Biosci. Biotechnol. Biochem., 64, 670-673 (2000).
2. Gaasterland, T., and Sensen, C. W., MAGPIE: automated genome interpretation. Trends Genet., 12, 76-78 (1996).
3. Frishman, D., Albermann, K., Hani, J., Heumann, K., Metanomski, A., Zollner, A., and Mewes, H. W., Functional and structural genomics using PEDANT. Bioinformatics, 17, 44-57 (2001).
4. Meyer, F., Goesmann, A., McHardy, A. C., Bartels, D., Bekel, T., Clausen, J., Kalinowski, J., Linke, B., Rupp, O., Giegerich, R., and Puhler, A., GenDB: an open source genome annotation system for prokaryote genomes. Nucleic Acids Res., 31, 2187-2195 (2003).
5. Vallenet, D., Labarre, L., Rouy, Z., Barbe, V., Bocs, S., Cruveiller, S., Lajus, A., Pascal, G., Scarpelli, C., and Medigue, C., MaGe: a microbial genome annotation system supported by synteny results. Nucleic Acids Res., 34, 53-65 (2006).
6. Delcher, A. L., Bratke, K. A., Powers, E. C., and Salzberg, S. L., Identifying bacterial genes and endosymbiont DNA with Glimmer. Bioinformatics, 23, 673-679 (2007).
7. Falquet, L., Pagni, M., Bucher, P., Hulo, N., Sigrist, C. J., Hofmann, K., and Bairoch, A., The PROSITE database, its status in 2002. Nucleic Acids Res., 30, 235-238 (2002).
8. Altschul, S. F., Madden, T. L., Schaffer, A. A., Zhang, J., Zhang, Z., Miller, W., and Lipman, D. J., Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res., 25, 3389-3402 (1997).
9. Tatusov, R. L., Fedorova, N. D., Jackson, J. D., Jacobs, A. R., Kiryutin, B., Koonin, E. V., Krylov, D. M., Mazumder, R., Mekhedov, S. L., Nikolskaya, A. N., Rao, B. S., Smirnov, S., Sverdlov, A. V., Vasudevan, S., Wolf, Y. I., Yin, J. J., and Natale, D. A., The COG database: an updated version includes eukaryotes. BMC Bioinformatics, 4, 41 (2003).
10. Harris, M. A., Clark, J., Ireland, A., Lomax, J., Ashburner, M., Foulger, R., Eilbeck, K., Lewis, S., Marshall, B., Mungall, C., Richter, J., Rubin, G. M., Blake, J. A., Bult, C., Dolan, M., Drabkin, H., Eppig, J. T., Hill, D. P., Ni, L., Ringwald, M., Balakrishnan, R., Cherry, J. M., Christie, K. R., Costanzo, M. C., Dwight, S. S., Engel, S., Fisk, D. G., Hirschman, J. E., Hong, E. L., Nash, R. S., Sethuraman, A., Theesfeld, C. L., Botstein, D., Dolinski, K., Feierbach, B., Berardini, T., Mundodi, S., Rhee, S. Y., Apweiler, R., Barrell, D., Camon, E., Dimmer, E., Lee, V., Chisholm, R., Gaudet, P., Kibbe, W., Kishore, R., Schwarz, E. M., Sternberg, P., Gwinn, M., Hannick, L., Wortman, J., Berriman, M., Wood, V., de la Cruz, N., Tonellato, P., Jaiswal, P., Seigfried, T., and White, R., The gene ontology (GO) database and informatics resource. Nucleic Acids Res., 32, D258-261 (2004).
11. Lowe, T. M., and Eddy, S. R., tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res., 25, 955-964 (1997).
12. Lobry, J. R., Asymmetric substitution patterns in the two DNA strands of bacteria. Mol. Biol. Evol., 13, 660-665 (1996).
13. Ogata, H., Goto, S., Sato, K., Fujibuchi, W., Bono, H., and Kanehisa, M., KEGG: Kyoto encyclopedia of genes and genomes. Nucleic Acids Res., 27, 29-34 (1999).
14. Kim, Y. R., Lee, S. E., Kim, C. M., Kim, S. Y., Shin, E. K., Shin, D. H., Chung, S. S., Choy, H. E., Progulske-Fox, A., Hillman, J. D., Handfield, M., and Rhee, J. H., Characterization and pathogenic significance of Vibrio vulnificus antigens preferentially expressed in septicemic patients. Infect. Immun., 71, 5461-5471 (2003).
15. Parajuli, N., Basnet, D. B., Chan Lee, H., Sohng, J. K., and Liou, K., Genome analyses of Streptomyces peucetius ATCC 27952 for the identification and comparison of cytochrome P450 complement with other Streptomyces. Arch. Biochem. Biophys., 425, 233-241 (2004).