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Cited by 18,818

The DOI matches its Crossref record; 3 of the 3 references it cites were found in a registry or an index.

Prokka: rapid prokaryotic genome annotation

Seemann, Torsten·2014·Bioinformatics
DOI 10.1093/bioinformatics/btu153
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Abstract

Summary: The multiplex capability and high yield of current day DNA-sequencing instruments has made bacterial whole genome sequencing a routine affair. The subsequent de novo assembly of reads into contigs has been well addressed. The final step of annotating all relevant genomic features on those contigs can be achieved slowly using existing web- and email-based systems, but these are not applicable for sensitive data or integrating into computational pipelines. Here we introduce Prokka, a command line software tool to fully annotate a draft bacterial genome in about 10 min on a typical desktop computer. It produces standards-compliant output files for further analysis or viewing in genome browsers. Availability and implementation: Prokka is implemented in Perl and is freely available under an open source GPLv2 license from http://vicbioinformatics.com/ . Contact: torsten.seemann@monash.edu

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Cites

Show all 3 references

Research works printed but not linked: 12

  1. Aziz, 2008, The RAST Server: rapid annotations using subsystems technology, BMC Genomics, 9, 75, 10.1186/1471-2164-9-75 · DOI · Paper page
  2. Apweiler, 2004, UniProt: the universal protein knowledgebase, Nucleic Acids Res., 32, D115, 10.1093/nar/gkh131 · DOI
  3. Chaudhuri, 2008, xBASE2: a comprehensive resource for comparative bacterial genomics, Nucleic Acids Res., 36, D543, 10.1093/nar/gkm928 · DOI
  4. Haft, 2013, TIGRFAMs and genome properties in 2013, Nucleic Acids Res., 41, D387, 10.1093/nar/gks1234 · DOI · Paper page
  5. Hyatt, 2010, Prodigal: prokaryotic gene recognition and translation initiation site identification, BMC Bioinformatics, 11, 119, 10.1186/1471-2105-11-119 · DOI · Paper page
  6. Kolbe, 2011, Fast filtering for RNA homology search, Bioinformatics, 27, 3102, 10.1093/bioinformatics/btr545 · DOI
  7. Lagesen, 2007, RNAmmer: consistent and rapid annotation of ribosomal RNA genes, Nucleic Acids Res., 35, 3100, 10.1093/nar/gkm160 · DOI
  8. Laslett, 2004, ARAGORN, a program to detect tRNA genes and tmRNA genes in nucleotide sequences, Nucleic Acids Res., 32, 11, 10.1093/nar/gkh152 · DOI · Paper page
  9. Punta, 2012, The Pfam protein families database, Nucleic Acids Res., 40, D290, 10.1093/nar/gkr1065 · DOI · Paper page
  10. Richardson, 2013, The automatic annotation of bacterial genomes, Brief. Bioinform., 14, 1, 10.1093/bib/bbs007 · DOI
  11. Stewart, 2009, DIYA: a bacterial annotation pipeline for any genomics lab, Bioinformatics, 25, 962, 10.1093/bioinformatics/btp097 · DOI
  12. Tange, 2011, GNU Parallel—The Command-Line Power Tool

Cited by

Metadata

Authors
Seemann, T.
Venue
Bioinformatics
Publisher
Oxford University Press (OUP)
Published
2014-03-18
Volume
30
Issue
14
Pages
2068-2069
ISSN
  • 1367-4803 (ISSN-L)
  • 1367-4811
DOI
10.1093/bioinformatics/btu153
OpenAlex
W2096093282
Cited by
18,818
References
3
FWCI
160.98
Type
journal article
Language
en
Open access
closed

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