A semi-automated genome annotation comparison and integration scheme

BMC Bioinformatics

Volumn 14, Issue 1, 2013, Pages

  Liu, Zhe ^a   Ma, Hongwu ^a,b,c   Goryanin, Igor ^a,c  

^a UNIVERSITY OF EDINBURGH   (United Kingdom)

^b Chinese Academy of Sciences   (China)

^c OKINAWA INSTITUTE OF SCIENCE AND TECHNOLOGY GRADUATE UNIVERSITY   (Japan)

Author keywords

Automated annotation services; Genome annotation comparison; Genome annotation determination

Indexed keywords

AUTOMATED ANNOTATION SERVICES; COMPARISON RESULT; DIFFERENT SERVICES; FUNCTIONAL ANNOTATION; GENOME ANNOTATION; INTEGRATION SCHEME; SEMI-AUTOMATED; SEMI-AUTOMATICS;

AUTOMATION; DECISION TREES;

GENES;

ARCOBACTER; ARCOBACTER BUTZLERI;

ARCOBACTER; ARTICLE; BACTERIAL GENE; BACTERIAL GENOME; CHROMOSOME MAP; ESCHERICHIA COLI; GENETICS; GENOMICS; METHODOLOGY; MOLECULAR GENETICS;

ARCOBACTER; CHROMOSOME MAPPING; ESCHERICHIA COLI; GENES, BACTERIAL; GENOME, BACTERIAL; GENOMICS; MOLECULAR SEQUENCE ANNOTATION;

EID: 84878368775     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-14-172     Document Type: Article

References (25)

1. Illunima Inc DNA sequencing with Solexa technology 2007, http://www.plantsciences.ucdavis.edu/bit150/2006/JD_Lecture/Lecture%201%20Databases/Solexa_DNAsequencing.pdf, Illunima Inc.
2. Margulies M, Egholm M, Altman WE, Attiya S, Bader JS, Bemben LA, Berka J, Braverman MS, Chen YJ, Chen Z. Genome sequencing in microfabricated high-density picolitre reactors. Nature 2005, 437(7057):376-380. 1464427, 16056220.
3. Stothard P, Wishart DS. Automated bacterial genome analysis and annotation. Curr Opin Microbiol 2006, 9(5):505-510. 10.1016/j.mib.2006.08.002, 16931121.
4. Markowitz VM, Szeto E, Palaniappan K, Grechkin Y, Chu K, Chen IM, Dubchak I, Anderson I, Lykidis A, Mavromatis K. The integrated microbial genomes (IMG) system in 2007: data content and analysis tool extensions. Nucleic Acids Res 2008, 36(Database issue):D528-533. 2238897, 17933782.
5. Aziz R, Bartels D, Best A, DeJongh M, Disz T, Edwards R, Formsma K, Gerdes S, Glass E, Kubal M. The RAST Server: Rapid Annotations using Subsystems Technology. BMC Genomics 2008, 9(1):75. 10.1186/1471-2164-9-75, 2265698, 18261238.
6. Overbeek R, Bartels D, Vonstein V, Meyer F. Annotation of bacterial and archaeal genomes: improving accuracy and consistency. Chem Rev 2007, 107(8):3431-3447. 10.1021/cr068308h, 17658903.
7. JCVI Annotation Service http://www.jcvi.org/cms/research/projects/annotation-service/, JCVI Annotation Service.
8. IGS Annotation Service http://ae.igs.umaryland.edu/cgi/, IGS Annotation Service.
9. Iliopoulos I, Tsoka S, Andrade MA, Enright AJ, Carroll M, Poullet P, Promponas V, Liakopoulos T, Palaios G, Pasquier C. Evaluation of annotation strategies using an entire genome sequence. Bioinformatics 2003, 19(6):717-726. 10.1093/bioinformatics/btg077, 12691983.
10. Bakke P, Carney N, DeLoache W, Gearing M, Ingvorsen K, Lotz M, McNair J, Penumetcha P, Simpson S, Voss L. Evaluation of Three Automated Genome Annotations for Halorhabdus utahensis. PLoS One 2009, 4(7):e6291. 10.1371/journal.pone.0006291, 2707008, 19617911.
11. Richardson EJ, Watson M. The automatic annotation of bacterial genomes. Brief Bioinform 2013, 14(1):1-12. 10.1093/bib/bbs007, 3548604, 22408191.
12. The Gene Ontology's Reference Genome Project: a unified framework for functional annotation across species. PLoS Comput Biol 2009, 5(7):e1000431. 10.1371/journal.pcbi.1000431, 2699109, 19578431.
13. Kasukawa T, Furuno M, Nikaido I, Bono H, Hume DA, Bult C, Hill DP, Baldarelli R, Gough J, Kanapin A. Development and evaluation of an automated annotation pipeline and cDNA annotation system. Genome Res 2003, 13(6B):1542-1551. 403710, 12819153.
14. Miller WG, Parker CT, Rubenfield M, Mendz GL, Wösten MMSM, Ussery DW, Stolz JF, Binnewies TT, Hallin PF, Wang G. The Complete Genome Sequence and Analysis of the Epsilonproteobacterium Arcobacter butzleri. PLoS One 2007, 2(12):e1358. 10.1371/journal.pone.0001358, 2147049, 18159241.
15. Bird S, Klein E, Loper E. Natural Language Processing with Python. O'Reilly Media 2009, http://nltk.org/book.
16. Christiane F. WordNet: An Electronic Lexical Database 1998, Cambridge, Massachusetts: The MIT Press.
17. NCBI data ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/gene_info.gz.
18. Pfam data ftp://ftp.sanger.ac.uk/pub/databases/Pfam/releases/Pfam26.0/database_files/.
19. Schneider A, Dessimoz C, Gonnet GH. OMA Browser-Exploring orthologous relations across 352 complete genomes. Bioinformatics 2007, 23(16):2180-2182. 10.1093/bioinformatics/btm295, 17545180.
20. Dessimoz C, Cannarozzi G, Gil M, Margadant D, Roth A, Schneider A, Gonnet G. OMA, A Comprehensive, Automated Project for the Identification of Orthologs from Complete Genome Data: Introduction and First Achievements Comparative Genomics. 2005, 3678:61-72. Heidelberg: Springer Berlin, McLysaght A, Huson D.
21. Manning CD, Raghavan P, Schuetze H. Introduction to Information Retrieval 2008, Cambridge University Press.
22. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol 1990, 215(3):403-410.
23. Krogh A, Larsson B, von Heijne G, Sonnhammer ELL. Predicting transmembrane protein topology with a hidden markov model: application to complete genomes. J Mol Biol 2001, 305(3):567-580. 10.1006/jmbi.2000.4315, 11152613.
24. Haft DH, Selengut JD, White O. The TIGRFAMs database of protein families. Nucleic Acids Res 2003, 31(1):371-373. 10.1093/nar/gkg128, 165575, 12520025.
25. Keseler IM, Collado-Vides J, Santos-Zavaleta A, Peralta-Gil M, Gama-Castro S, Muniz-Rascado L, Bonavides-Martinez C, Paley S, Krummenacker M, Altman T. EcoCyc: a comprehensive database of Escherichia coli biology. Nucleic Acids Res 2011, 39(Database issue):D583-590. 3013716, 21097882.