MUTAGEN: multi-user tool for annotating genomes - PubMed (original) (raw)

MUTAGEN: multi-user tool for annotating genomes

Kim Brügger et al. Bioinformatics. 2003.

Abstract

Summary: MUTAGEN is a free prokaryotic annotation system. It offers the advantages of genome comparison, graphical sequence browsers, search facilities and open-source for user-specific adjustments. The web-interface allows several users to access the system from standard desktop computers. The Sulfolobus acidocaldarius genome, and several plasmids and viruses have so far been analysed and annotated using MUTAGEN.

Availability: MUTAGEN is released as open-source software under GPL. The code is available for download and/or contribution at http://dac.molbio.ku.dk/bioinformatics/MUTAGEN/

PubMed Disclaimer

Similar articles

• Genquire: genome annotation browser/editor.
  Wilkinson MD, Block D, Crosby WL. Wilkinson MD, et al. Bioinformatics. 2002 Oct;18(10):1398-9. doi: 10.1093/bioinformatics/18.10.1398. Bioinformatics. 2002. PMID: 12376386
• BugView: a browser for comparing genomes.
  Leader DP. Leader DP. Bioinformatics. 2004 Jan 1;20(1):129-30. doi: 10.1093/bioinformatics/btg383. Bioinformatics. 2004. PMID: 14693822
• G-language Genome Analysis Environment: a workbench for nucleotide sequence data mining.
  Arakawa K, Mori K, Ikeda K, Matsuzaki T, Kobayashi Y, Tomita M. Arakawa K, et al. Bioinformatics. 2003 Jan 22;19(2):305-6. doi: 10.1093/bioinformatics/19.2.305. Bioinformatics. 2003. PMID: 12538262
• Integrated analysis of the genome and the transcriptome by FANTOM.
  Katayama S, Kanamori M, Hayashizaki Y. Katayama S, et al. Brief Bioinform. 2004 Sep;5(3):249-58. doi: 10.1093/bib/5.3.249. Brief Bioinform. 2004. PMID: 15383211 Review.
• A bioinformatician's guide to metagenomics.
  Kunin V, Copeland A, Lapidus A, Mavromatis K, Hugenholtz P. Kunin V, et al. Microbiol Mol Biol Rev. 2008 Dec;72(4):557-78, Table of Contents. doi: 10.1128/MMBR.00009-08. Microbiol Mol Biol Rev. 2008. PMID: 19052320 Free PMC article. Review.

Cited by

• Familial relationships in hyperthermo- and acidophilic archaeal viruses.
  Happonen LJ, Redder P, Peng X, Reigstad LJ, Prangishvili D, Butcher SJ. Happonen LJ, et al. J Virol. 2010 May;84(9):4747-54. doi: 10.1128/JVI.02156-09. Epub 2010 Feb 17. J Virol. 2010. PMID: 20164227 Free PMC article.
• Stygiolobus rod-shaped virus and the interplay of crenarchaeal rudiviruses with the CRISPR antiviral system.
  Vestergaard G, Shah SA, Bize A, Reitberger W, Reuter M, Phan H, Briegel A, Rachel R, Garrett RA, Prangishvili D. Vestergaard G, et al. J Bacteriol. 2008 Oct;190(20):6837-45. doi: 10.1128/JB.00795-08. Epub 2008 Aug 22. J Bacteriol. 2008. PMID: 18723627 Free PMC article.
• Structure of the acidianus filamentous virus 3 and comparative genomics of related archaeal lipothrixviruses.
  Vestergaard G, Aramayo R, Basta T, Häring M, Peng X, Brügger K, Chen L, Rachel R, Boisset N, Garrett RA, Prangishvili D. Vestergaard G, et al. J Virol. 2008 Jan;82(1):371-81. doi: 10.1128/JVI.01410-07. Epub 2007 Oct 17. J Virol. 2008. PMID: 17942536 Free PMC article.
• The genome of Hyperthermus butylicus: a sulfur-reducing, peptide fermenting, neutrophilic Crenarchaeote growing up to 108 degrees C.
  Brügger K, Chen L, Stark M, Zibat A, Redder P, Ruepp A, Awayez M, She Q, Garrett RA, Klenk HP. Brügger K, et al. Archaea. 2007 May;2(2):127-35. doi: 10.1155/2007/745987. Archaea. 2007. PMID: 17350933 Free PMC article.
• The Sulfolobus database.
  Brügger K. Brügger K. Nucleic Acids Res. 2007 Jan;35(Database issue):D413-5. doi: 10.1093/nar/gkl847. Epub 2006 Nov 6. Nucleic Acids Res. 2007. PMID: 17088281 Free PMC article.

Publication types

MeSH terms

LinkOut - more resources

• Full Text Sources

  • Ovid Technologies, Inc.
  • Silverchair Information Systems