ReseqChip: automated integration of multiple local context probe data from the MitoChip array in mitochondrial DNA sequence assembly

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urn:nbn:de:bvb:355-epub-306621 Copy

Thieme, Marian ; Lottaz, Claudio ; Niederstätter, Harald ; Parson, Walther ; Spang, Rainer ; Oefner, Peter J.

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Date of publication of this fulltext: 18 Aug 2014 09:47

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Details

Item type:	Article
Date:	December 2009
Institutions:	Medicine > Institut für Funktionelle Genomik > Lehrstuhl für Funktionelle Genomik (Prof. Oefner) Medicine > Institut für Funktionelle Genomik > Lehrstuhl für Statistische Bioinformatik (Prof. Spang)
Identification Number:	Value Type 10508508 PubMed ID 10.1186/1471-2105-10-440 DOI
Classification:	Notation Type Base Sequence MESH Computational Biology/methods MESH DNA, Mitochondrial/chemistry MESH Genome, Mitochondrial/genetics MESH Sequence Analysis, DNA MESH Software MESH
Dewey Decimal Classification:	600 Technology > 610 Medical sciences Medicine
Status:	Published
Refereed:	Yes, this version has been refereed
Created at the University of Regensburg:	Partially
Item ID:	30662

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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 ...

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.

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