Software
ReseqChip: Automated integration of multiple local context probe data from the MitoChip array in mitochondrial DNA sequence assembly
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* Corresponding author: Marian Thieme marian.thieme@klinik.uni-regensburg.de
1 Institute of Functional Genomics, University of Regensburg, Josef-Engert-Str. 9, D-93053 Regensburg, Germany
2 Institute of Legal Medicine, Innsbruck Medical University, Muellerstrasse 44, A-6020 Innsbruck, Austria
BMC Bioinformatics 2009, 10:440 doi:10.1186/1471-2105-10-440
Published: 22 December 2009Abstract
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/ webcite.
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.