MitoZoa: A curated mitochondrial genome database of metazoans for comparative genomics studies

Lupi, Renato; Meo, Paolo D’Onorio De; Picardi, Ernesto; D’Antonio, Mattia; Paoletti, Daniele; Castrignanò, Tiziana; Pesole, Graziano; Gissi, Carmela

doi:10.1016/j.mito.2010.01.004

Cited by 46 publications

(35 citation statements)

References 39 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The entire database Mitozoa (Lupi et al, 2010), a manually curated collection of all known complete or nearly complete mitochondrial genomes of Metazoa, was downloaded as of version 8.1 (July 2011). Original gene annotations were retained, and non-gene regions were reannotated as short unassigned regions (SUN, if b500 bp) and long unassigned regions (LUN, if ≥500 bp).…”

Section: Datasetsmentioning

confidence: 99%

Repeated regions in mitochondrial genomes: Distribution, origin and evolutionary significance

2012

View full text Add to dashboard Cite

Section: Datasetsmentioning

confidence: 99%

Repeated regions in mitochondrial genomes: Distribution, origin and evolutionary significance

2012

View full text Add to dashboard Cite

“…Additional comparisons with the 2387 mitogenomes of the MitoZoa database [13] that are also contained in RefSeq have been carried out. The suffix tree was constructed with the original sequences and their reverse complements.…”

Section: Methodsmentioning

confidence: 99%

“…The MitoZoa database contains improved annotations that are obtained manually following a specified protocol [13]. Several tools for the automatic annotation of mitogenomes are available.…”

Section: Introductionmentioning

confidence: 99%

Local Similarity Search to Find Gene Indicators in Mitochondrial Genomes

Moritz

Bernt

Middendorf

2014

Biology

View full text Add to dashboard Cite

Given a set of nucleotide sequences we consider the problem of identifying conserved substrings occurring in homologous genes in a large number of sequences. The problem is solved by identifying certain nodes in a suffix tree containing all substrings occurring in the given nucleotide sequences. Due to the large size of the targeted data set, our approach employs a truncated version of suffix trees. Two methods for this task are introduced: (1) The annotation guided marker detection method uses gene annotations which might contain a moderate number of errors; (2) The probability based marker detection method determines sequences that appear significantly more often than expected. The approach is successfully applied to the mitochondrial nucleotide sequences, and the corresponding annotations that are available in RefSeq for 2989 metazoan species. We demonstrate that the approach finds appropriate substrings.

show abstract

“…RefSeq contains mitogenomes of 1,627 Chordata, 376 Arthropoda, and 104 Mollusca. The policy of RefSeq to provide "only one example of each natural biological molecule for major organisms" (Mizrachi, 2007) is a potential problem for taxa with doubly uniparental inheritance, e.g., many Mollusca or cryptic species (Lupi et al, 2010). Several databases have been built upon the GenBank or RefSeq with the aim of improving annotation and data quality.…”

Section: Databasesmentioning

confidence: 99%

Bioinformatics methods for the comparative analysis of metazoan mitochondrial genome sequences

Bernt

Braband

Middendorf

et al. 2013

Molecular Phylogenetics and Evolution

View full text Add to dashboard Cite

In this review we provide an overview of various bioinformatics methods and tools for the analysis of metazoan mitochondrial genomes. We compare available dedicated databases and present current tools for accurate genome annotation, identification of protein coding genes, and determination of tRNA and rRNA models.We also evaluate various tools and models for phylogenetic tree inference using gene order or sequence based data. As for gene order based methods, we compare rearrangement based and gene cluster based methods for gene order rearrangement analysis. As for sequence based methods, we give special emphasis to substitution models or data treatment that reduces certain systematic biases that are typical for metazoan mitogenomes such as within genome and/or among lineage compositional heterogeneity.

show abstract

MitoZoa: A curated mitochondrial genome database of metazoans for comparative genomics studies

Cited by 46 publications

References 39 publications

Repeated regions in mitochondrial genomes: Distribution, origin and evolutionary significance

Repeated regions in mitochondrial genomes: Distribution, origin and evolutionary significance

Local Similarity Search to Find Gene Indicators in Mitochondrial Genomes

Bioinformatics methods for the comparative analysis of metazoan mitochondrial genome sequences

Contact Info

Product

Resources

About