title: Density-based hierarchical clustering of pyro-sequences on a large scale--the case of fungal ITS1.
abstract: BACKGROUND
  Analysis of millions of pyro-sequences is currently playing a crucial role in the advance of environmental microbiology. Taxonomy-independent, i.e. unsupervised, clustering of these sequences is essential for the definition of Operational Taxonomic Units. For this application, reproducibility and robustness should be the most sought after qualities, but have thus far largely been overlooked.
  
  
  RESULTS
  More than 1 million hyper-variable internal transcribed spacer 1 (ITS1) sequences of fungal origin have been analyzed. The ITS1 sequences were first properly extracted from 454 reads using generalized profiles. Then, otupipe, cd-hit-454, ESPRIT-Tree and DBC454, a new algorithm presented here, were used to analyze the sequences. A numerical assay was developed to measure the reproducibility and robustness of these algorithms. DBC454 was the most robust, closely followed by ESPRIT-Tree. DBC454 features density-based hierarchical clustering, which complements the other methods by providing insights into the structure of the data.
  
  
  BACKGROUND
  An executable is freely available for non-commercial users at ftp://ftp.vital-it.ch/tools/dbc454. It is designed to run under MPI on a cluster of 64-bit Linux machines running Red Hat 4.x, or on a multi-core OSX system.
  
  
  BACKGROUND
  dbc454@vital-it.ch or nicolas.guex@isb-sib.ch.
authors.affiliation: Vital-IT Group, SIB Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland.
authors.forename: Marco
authors.initials: M
authors.lastname: Pagni
authors.forename: Hélène
authors.initials: H
authors.lastname: Niculita-Hirzel
authors.forename: Loïc
authors.initials: L
authors.lastname: Pellissier
authors.forename: Anne
authors.initials: A
authors.lastname: Dubuis
authors.forename: Ioannis
authors.initials: I
authors.lastname: Xenarios
authors.forename: Antoine
authors.initials: A
authors.lastname: Guisan
authors.forename: Ian R
authors.initials: IR
authors.lastname: Sanders
authors.forename: Jérôme
authors.initials: J
authors.lastname: Goudet
authors.forename: Nicolas
authors.initials: N
authors.lastname: Guex
mesh_terms: D000465:Algorithms; D016000:Cluster Analysis; D004271:DNA, Fungal / Q000235:genetics*; D021903:DNA, Ribosomal Spacer / Q000235:genetics*; D005658:Fungi / Q000145:classification* / Q000235:genetics / Q000302:isolation & purification; D015203:Reproducibility of Results; D012988:Soil Microbiology
chemical_list: D004271:DNA, Fungal; D021903:DNA, Ribosomal Spacer
references.citation: BMC Bioinformatics. 2010 Apr 13;11:187
references.pmid: 20388221
references.citation: Nucleic Acids Res. 2011 Aug;39(14):e95
references.pmid: 21596775
references.citation: Mol Biol Evol. 2013 Apr;30(4):772-80
references.pmid: 23329690
references.citation: Brief Bioinform. 2012 Jan;13(1):107-21
references.pmid: 21525143
references.citation: Bioinformatics. 2010 Oct 1;26(19):2460-1
references.pmid: 20709691
references.citation: Brief Bioinform. 2001 Mar;2(1):51-67
references.pmid: 11465063
references.citation: Genome Biol. 2007;8(7):R143
references.pmid: 17659080
references.citation: Nat Methods. 2009 Sep;6(9):639-41
references.pmid: 19668203
references.citation: Protein Sci. 1994 Jan;3(1):139-46
references.pmid: 7511453
references.citation: Bioinformatics. 2011 Aug 15;27(16):2194-200
references.pmid: 21700674
references.citation: Brief Bioinform. 2002 Sep;3(3):265-74
references.pmid: 12230035
references.citation: Bioinformatics. 2012 Nov 15;28(22):2891-7
references.pmid: 22962346
references.citation: BMC Microbiol. 2010 Jul 09;10:189
references.pmid: 20618939
references.citation: Trends Genet. 2000 Jun;16(6):276-7
references.pmid: 10827456