MitoBamAnnotator: A web-based tool for detecting and annotating heteroplasmy in human mitochondrial DNA sequences.

The use of Next-Generation Sequencing of mitochondrial DNA is becoming widespread in biological and clinical research. This, in turn, creates a need for a convenient tool that detects and analyzes heteroplasmy. Here we present MitoBamAnnotator, a user friendly web-based tool that allows maximum flexibility and control in heteroplasmy research. MitoBamAnnotator provides the user with a comprehensively annotated overview of mitochondrial genetic variation, allowing for an in-depth analysis with no prior knowledge in programming.

[1]  B. C. Levin,et al.  MitoAnalyzer, a computer program and interactive web site to determine the effects of single nucleotide polymorphisms and mutations in human mitochondrial DNA. , 2002, Mitochondrion.

[2]  Gonçalo R. Abecasis,et al.  The Sequence Alignment/Map format and SAMtools , 2009, Bioinform..

[3]  Tal Pupko,et al.  ConSurf 2010: calculating evolutionary conservation in sequence and structure of proteins and nucleic acids , 2010, Nucleic Acids Res..

[4]  S. Henikoff,et al.  Amino acid substitution matrices from protein blocks. , 1992, Proceedings of the National Academy of Sciences of the United States of America.

[5]  Hans-Jürgen Bandelt,et al.  A Critical Reassessment of the Role of Mitochondria in Tumorigenesis , 2005, PLoS medicine.

[6]  Günther Specht,et al.  HaploGrep: a fast and reliable algorithm for automatic classification of mitochondrial DNA haplogroups , 2011, Human mutation.

[7]  Sha Tang,et al.  Characterization of mitochondrial DNA heteroplasmy using a parallel sequencing system. , 2010, BioTechniques.

[8]  D. Mishmar,et al.  MtDNA mutation pattern in tumors and human evolution are shaped by similar selective constraints. , 2009, Genome research.

[9]  D. Altshuler,et al.  A map of human genome variation from population-scale sequencing , 2010, Nature.

[10]  D. Dressman,et al.  Heteroplasmic mitochondrial DNA mutations in normal and tumor cells , 2010, Nature.

[11]  Mark Stoneking,et al.  Detecting heteroplasmy from high-throughput sequencing of complete human mitochondrial DNA genomes. , 2010, American journal of human genetics.

[12]  A. Nekrutenko,et al.  Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences , 2010, Genome Biology.

[13]  Manfred Kayser,et al.  Updated comprehensive phylogenetic tree of global human mitochondrial DNA variation , 2009, Human mutation.

[14]  Eloisa Arbustini,et al.  Mitochondrial DNA Variant Discovery and Evaluation in Human Cardiomyopathies through Next-Generation Sequencing , 2010, PloS one.

[15]  Marty C. Brandon,et al.  Effects of Purifying and Adaptive Selection on Regional Variation in Human mtDNA , 2004, Science.

[16]  A. Templeton,et al.  Mitochondrial bioenergetics as a major motive force of speciation , 2009, BioEssays : news and reviews in molecular, cellular and developmental biology.