mtDNA GeneExtractor: A computer tool for mtDNA gene/region information extraction
Fernando Freitas, Sandra Oliveira, Ricardo Rocha and LuĂsa Pereira
2009
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 shows no evidence for selection in the 13 mtDNA
protein-coding genes.
Bibtex
@Article{freitas-mitochondrion09,
author = {F. Freitas and S. Oliveira and R. Rocha and L. Pereira},
title = {{mtDNA GeneExtractor: A computer tool for mtDNA gene/region information extraction}},
journal = {Mitochondrion Journal},
pages = {36--40},
volume = {9},
number = {1},
year = {2009},
}
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