EuGene-PP: A next-generation automated annotation pipeline for prokaryotic genomes

Bioinformatics

Volumn 30, Issue 18, 2014, Pages 2659-2661

  Sallet, Erika ^a   Gouzy, Jérôme ^a   Schiex, Thomas ^b  

^a CNRS   (France)

^b CEMAGREF   (France)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; AUTOMATION; BACTERIAL GENOME; BACTERIUM; COMPUTER PROGRAM; GENETICS; GENOMICS; METHODOLOGY; MOLECULAR GENETICS; SEQUENCE ANALYSIS; TRANSCRIPTION INITIATION SITE;

AUTOMATION; BACTERIA; GENOME, BACTERIAL; GENOMICS; MOLECULAR SEQUENCE ANNOTATION; SEQUENCE ANALYSIS, RNA; SOFTWARE; TRANSCRIPTION INITIATION SITE;

EID: 84907482617     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btu366     Document Type: Article

References (14)

1. Delcher, A.L. et al. (2007) Identifying bacterial genes and endosymbiont DNA with Glimmer. Bioinformatics, 23, 673-679.
2. Foissac, S. et al. (2008) Genome annotation in plants and fungi: EuGene as a model platform. Curr. Bioinform., 3, 87-97.
3. Goecks, J. et al. (2010) Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences. Genome Biol., 11, R86.
4. Griffiths-Jones, S. (2005) Annotating non-coding RNAs with Rfam. Curr. Protoc. Bioinform., 12, 125.
5. Hyatt, D. et al. (2010) Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics, 11, 119.
6. Kröger, C. et al. (2013) An infection-relevant transcriptomic compendium for Salmonella enterica Serovar Typhimurium. Cell Host Microbe, 14, 683-695.
7. Lagesen, K. et al. (2007) RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res., 35, 3100-3108.
8. Li, S. et al. (2013) Directional RNA-seq reveals highly complex condition-dependent transcriptomes in E.coli k12 through accurate full-length transcripts assembling. BMC Genomics, 14, 520.
9. Lowe, T.M. and Eddy, S.R. (1997) tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res., 25, 955-964.
10. Martin, J. et al. (2010) Bacillus anthracis genome organization in light of whole transcriptome sequencing. BMC Bioinformatics, 11 (Suppl 3), S10.
11. Moody, M.J. et al. (2013) Comparative analysis of non-coding rnas in the antibiotic-producing streptomyces bacteria. BMC Genomics, 14, 558.
12. Nicolas, P. et al. (2012) Condition-dependent transcriptome reveals high-level regulatory architecture in Bacillus subtilis. Science, 335, 1103-1106.
13. Sallet, E. et al. (2013) Next-generation annotation of prokaryotic genomes with eugene-p: Application to Sinorhizobium meliloti 2011. DNA Res., 20, 339-354.
14. Zickmann, F. et al. (2014) GIIRA-RNA-seq driven gene finding incorporating ambiguous reads. Bioinformatics, 30, 606-613.