Journal ArticleDOI
MITOS: Improved de novo metazoan mitochondrial genome annotation
Matthias Bernt,Alexander Donath,Frank Jühling,Frank Jühling,Fabian Externbrink,Catherine Florentz,Guido Fritzsch,Joern Pütz,Martin Middendorf,Peter F. Stadler +9 more
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TLDR
The MITOS pipeline is designed to compute a consistent de novo annotation of the mitogenomic sequences and it is shown that the results of MITOS match RefSeq and MitoZoa in terms of annotation coverage and quality.About:
This article is published in Molecular Phylogenetics and Evolution.The article was published on 2013-11-01. It has received 3323 citations till now. The article focuses on the topics: RefSeq.read more
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Complete mitochondrial genome and phylogeny of Microhyla butleri (Amphibia: Anura: Microhylidae)
TL;DR: The whole mitogenome of M. butleri will serve as a useful dataset for studying the genetics, systematics and phylogenetic relationships of the Microhyla species in particular, and MicrohYLidae in general.
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Information from the mitochondrial genomes of two egg parasitoids, Gonatocerus sp. and Telenomus sp., reveals a controversial phylogenetic relationship between Mymaridae and Scelionidae
TL;DR: The taxonomic status and phylogenetic affinities of Mymaridae and Scelionidae are controversial, based on similarities between these families in the characteristics of adults, larvae, and eggs as discussed by the authors.
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Mitochondrial phylogenomics provides insights into the phylogeny and evolution of spiders (Arthropoda: Araneae)
TL;DR: This study, the largest mitochondrial phylogenomics analysis of spiders to date, highlights the usefulness of mitogenomic data not only for providing efficient phylogenetic signals for spider phylogeny, but also for characterizing trait diversification in spider evolution.
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The complete mitochondrial genomes of two vent squat lobsters, Munidopsis lauensis and M. verrilli: Novel gene arrangements and phylogenetic implications.
TL;DR: The phylogenetic analyses based on both gene order data and nucleotide sequences (PCGs and rRNAs) revealed that the two species were closely related to Shinkaia crosnieri.
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Characterization of mitochondrial genomes of three Andrena bees (Apoidea: Andrenidae) and insights into the phylogenetics.
TL;DR: Three mitochondrial genomes (mitogenomes) of Andrena species, which are the pollinators of Camellia oleifera, present identical gene rearrangement events, including local inversion (trnR) and gene shuffling ( trnQ/trnM, trnK/ trnD, and trnW/trNC-trnY).
References
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Basic Local Alignment Search Tool
TL;DR: A new approach to rapid sequence comparison, basic local alignment search tool (BLAST), directly approximates alignments that optimize a measure of local similarity, the maximal segment pair (MSP) score.
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tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence.
Todd M. Lowe,Sean R. Eddy +1 more
TL;DR: A program is described, tRNAscan-SE, which identifies 99-100% of transfer RNA genes in DNA sequence while giving less than one false positive per 15 gigabases.
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NCBI Reference Sequence (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins
TL;DR: The National Center for Biotechnology Information Reference Sequence (RefSeq) database provides a non-redundant collection of sequences representing genomic data, transcripts and proteins that pragmatically includes sequence data that are currently publicly available in the archival databases.
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Biopython: freely available Python tools for computational molecular biology and bioinformatics
Peter J. A. Cock,Tiago Antao,Jeffrey T. Chang,Brad Chapman,Cymon J. Cox,Andrew Dalke,Iddo Friedberg,Thomas Hamelryck,Frank Kauff,Bartosz Wilczyński,Michiel J. L. de Hoon +10 more
TL;DR: Biopython includes modules for reading and writing different sequence file formats and multiple sequence alignments, dealing with 3D macro molecular structures, interacting with common tools such as BLAST, ClustalW and EMBOSS, accessing key online databases, as well as providing numerical methods for statistical learning.
Journal ArticleDOI
Automatic annotation of organellar genomes with DOGMA
TL;DR: The Dual Organellar GenoMe Annotator (DOGMA) automates the annotation of organellar genomes and allows the use of BLAST searches against a custom database, and conservation of basepairing in the secondary structure of animal mitochondrial tRNAs to identify and annotate genes.
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