title: ReseqChip: automated integration of multiple local context probe data from the MitoChip array in mitochondrial DNA sequence assembly.
abstract: BACKGROUND
  The Affymetrix MitoChip v2.0 is an oligonucleotide tiling array for the resequencing of the human mitochondrial (mt) genome. For each of 16,569 nucleotide positions of the mt genome it holds two sets of four 25-mer probes each that match the heavy and the light strand of a reference mt genome and vary only at their central position to interrogate all four possible alleles. In addition, the MitoChip v2.0 carries alternative local context probes to account for known mtDNA variants. These probes have been neglected in most studies due to the lack of software for their automated analysis.
  
  
  RESULTS
  We provide ReseqChip, a free software that automates the process of resequencing mtDNA using multiple local context probes on the MitoChip v2.0. ReseqChip significantly improves base call rate and sequence accuracy. ReseqChip is available at http://code.open-bio.org/svnweb/index.cgi/bioperl/browse/bioperl-live/trunk/Bio/Microarray/Tools/.
  
  
  CONCLUSIONS
  ReseqChip allows for the automated consolidation of base calls from alternative local mt genome context probes. It thereby improves the accuracy of resequencing, while reducing the number of non-called bases.
authors.affiliation: Institute of Functional Genomics, University of Regensburg, Josef-Engert-Str, 9, D-93053 Regensburg, Germany. marian.thieme@klinik.uni-regensburg.de
authors.forename: Marian
authors.initials: M
authors.lastname: Thieme
authors.forename: Claudio
authors.initials: C
authors.lastname: Lottaz
authors.forename: Harald
authors.initials: H
authors.lastname: Niederstätter
authors.forename: Walther
authors.initials: W
authors.lastname: Parson
authors.forename: Rainer
authors.initials: R
authors.lastname: Spang
authors.forename: Peter J
authors.initials: PJ
authors.lastname: Oefner
mesh_terms: D001483:Base Sequence; D019295:Computational Biology / Q000379:methods*; D004272:DNA, Mitochondrial / Q000737:chemistry*; D054629:Genome, Mitochondrial / Q000235:genetics*; D017422:Sequence Analysis, DNA; D012984:Software
chemical_list: D004272:DNA, Mitochondrial