Reannotation of hypothetical ORFs in plant pathogen Erwinia carotovora subsp. atroseptica SCRI1043

FEBS Journal

Volumn 275, Issue 1, 2008, Pages 198-206

  Chen, Ling Ling ^a   Ma, Bin Guang ^a   Gao, Na ^a  

^a SHANDONG UNIVERSITY OF TECHNOLOGY   (China)

Author keywords

Clusters of orthologous groups of proteins; Function assignment; Hypothetical ORFs; Plant pathogen; Principal component analysis

Indexed keywords

MEMBRANE PROTEIN;

ARTICLE; GENE CLUSTER; HYPOTHESIS; NONHUMAN; NUCLEOTIDE SEQUENCE; OPEN READING FRAME; ORTHOLOGY; PECTOBACTERIUM CAROTOVORUM; PLANT DISEASE; PRIORITY JOURNAL; SENSITIVITY AND SPECIFICITY; SEQUENCE ANALYSIS;

ERWINIA; GENES, BACTERIAL; GENOME, BACTERIAL; OPEN READING FRAMES; PLANT DISEASES;

BACTERIA (MICROORGANISMS); PECTOBACTERIUM ATROSEPTICUM;

EID: 37349109147     PISSN: 1742464X     EISSN: 17424658     Source Type: Journal    
DOI: 10.1111/j.1742-4658.2007.06190.x     Document Type: Article

References (23)

1. Nielsen P Krogh A (2005) Large-scale prokaryotic gene prediction and comparison to genome annotation. Bioinformatics 21, 4322 4329.
2. Skovgaard M, Jensen LJ, Brunak S, Ussery D Krogh A (2001) On the total number of genes and their length distribution in complete microbial genomes. Trends Genet 17, 425 428.
3. Bell KS, Sebaihia M, Pritchard L, Holden MT, Hyman LJ, Holeva MC, Thomson NR, Bentley SD, Churcher LJ, Mungall K et al. (2004) Genome sequence of the enterobacterial phytopathogen Erwinia carotovora subsp. atroseptica and characterization of virulence factors. Proc Natl Acad Sci USA 101, 11105 11110.
4. Pérombelon MCM (2002) Potato diseases caused by soft rot erwinias: an overview of pathogenesis. Plant Pathol 51, 1 12.
5. Toth IK, Bell KS, Holeva MC Birch PRJ (2003) Soft rot erwiniae: from genes to genomes. Mol Plant Pathol 4, 17 30.
6. Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, Miller W Lipman DJ (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25, 3389 3402.
7. Schäffer AA, Aravind L, Madden TL, Shavirin S, Spouge JL, Wolf YI, Koonin EV Altschul SF (2001) Improving the accuracy of PSI-BLAST protein database searches with composition-based statistics and other refinements. Nucleic Acids Res 29, 2994 3005.
8. Pearson WR (1990) Rapid and sensitive sequence comparison with FASTP and FASTA. Methods Enzymol 183, 63 98.
9. Mulder NJ, Apweiler R, Attwood TK, Bairoch A, Bateman A, Binns D, Bork P, Buillard V, Cerutti L, Copley R et al. (2007) New developments in the InterPro database. Nucleic Acids Res 35, D224 D228.
10. Kanehisa M, Goto S, Hattori M, Aoki-Kinoshita KF, Itoh M, Kawashima S, Katayama T, Araki M Hirakawa M (2006) From genomics to chemical genomics: new developments in KEGG. Nucleic Acids Res 34, D354 D357.
11. Zhang CT Zhang R (1991) Analysis of distribution of bases in the coding sequences by a diagrammatic technique. Nucleic Acids Res 19, 6313 6317.
12. Dillon WR Goldstein M (1984) Multivariate Analysis - Methods and Applications (Wiley Series in Probability and Mathematical Statistics). Wiley, New York, NY.
13. Trifonov EN (1987) Translation framing code and frame-monitoring mechanism as suggested by the analysis of mRNA and 16S rRNA nucleotide sequences. J Mol Biol 194, 643 652.
14. Zhang CT Chou KC (1994) A graphic approach to analyzing codon usage in 1562 E. coli protein coding sequences. J Mol Biol 238, 1 8.
15. Gupta SK, Majumdar S, Bhattacharya TK Ghosh TC (2000) Studies on the relationships between the synonymous codon usage and protein secondary structural units. Biochem Biophys Res Commun 269, 692 696.
16. Pan A, Dutta C Das J (1998) Codon usage in highly expressed genes of Haemophillus influenzae and Mycobacterium tuberculosis: translational selection versus mutational bias. Gene 215, 405 413.
17. Chiusano ML, Alvarez-Valin F, Di Giulio M, D'Onofrio G, Ammirato G, Colonna G Bernardi G (2000) Second codon positions of genes and the secondary structures of proteins. Relationships and implications for the origin of the genetic code. Gene 261, 63 69.
18. Tatusov RL, Koonin EV Lipman DJ (1997) A genomic perspective on protein families. Science 278, 631 637.
19. Tatusov RL, Fedorova ND, Jackson JD, Jacobs AR, Kiryutin B, Koonin EV, Krylov DM, Mazumder R, Mekhedov SL, Nikolskaya AN et al. (2003) The COG database: an updated version includes eukaryotes. BMC Bioinformatics 4, 41.
20. Chen LL Zhang CT (2003) Gene recognition from questionable ORFs in bacterial and archaeal genomes. J Biomol Struct Dyn 21, 99 110.
21. Guo FB, Ou HY Zhang CT (2003) ZCURVE: a new system for recognizing protein-coding genes in bacterial and archaeal genomes. Nucleic Acids Res 31, 1780 1789.
22. Zhang CT Wang J (2000) Recognition of protein coding genes in the yeast genome at better than 95% accuracy based on the Z curve. Nucleic Acids Res 28, 2804 2814.
23. Gao F Zhang CT (2004) Comparison of various algorithms for recognizing short coding sequences of human genes. Bioinformatics 20, 673 681.