title: MtDNA GeneExtractor: a computer tool for mtDNA gene/region information extraction.
abstract: The analysis of considerable numbers of DNA sequences is largely dependent on the development of simple software tools for automatically process the genetic data deposited on public databases. However, there are some difficulties in the automation process due to diverse synonyms being used as qualifiers for genes and some inconsistencies in gene locations between related Primate species, this fact happening even in the carefully curated database RefSeq. Here, we present mtDNA GeneEXtractor, a Windows based computer tool developed for the extraction of information for particular gene/regions from mammal mitochondrial DNA sequences deposited under GenBank format. The tool was quite efficient in retrieving organized information for comparative mtDNA gene/region diversity analyses when tested for the evaluation of transition/transversion ratios in humans and between Primates. Taking phylogenetic information into account to avoid redundancy due to ancestry-sharing, the transition/transversion ratios in the 13 protein-coding genes had a mean value of 12.46 for Primates (from 6.46 in ND2 to 17.04 in COX1) and higher (34.74) but more heterogeneous (ranging from 17.30 in ND5 to 74.39 in ND4) in a worldwide human database. The similar patterns of transition/transversion ratios in all positions and in only four fold degenerate positions show no evidence for selection in the 13 mtDNA protein-coding genes.
authors.affiliation: Instituto de Patologia e Imunologia Molecular da Universidade do Porto (IPATIMUP), R. Dr. Roberto Frias s/n, 4200-465 Porto, Portugal.
authors.forename: Fernando
authors.initials: F
authors.lastname: Freitas
authors.forename: Sandra
authors.initials: S
authors.lastname: Oliveira
authors.forename: Ricardo
authors.initials: R
authors.lastname: Rocha
authors.forename: Luísa
authors.initials: L
authors.lastname: Pereira
mesh_terms: D000818:Animals; D019295:Computational Biology / Q000379:methods*; D003196:Computer Graphics; D004272:DNA, Mitochondrial / Q000235:genetics* / Q000378:metabolism*; D030541:Databases, Genetic; D014644:Genetic Variation; D006801:Humans; D011323:Primates; D011381:Programming Languages; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software; D013045:Species Specificity; D014584:User-Computer Interface
chemical_list: D004272:DNA, Mitochondrial