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
Citations
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The Complete Mitochondrial Genome Sequences of the Philomycus bilineatus (Stylommatophora: Philomycidae) and Phylogenetic Analysis.
TL;DR: The results indicated that P. bilineatus shares a close ancestry with Meghimatium bilineatum, and it seems more appropriate to reclassify it as Arionoidea rather than Limacoidea, as previously thought.
Journal ArticleDOI
The conserved mitochondrial genome of the jewel beetle (Coleoptera: Buprestidae) and its phylogenetic implications for the suborder Polyphaga.
TL;DR: The mt genome of a species in the family Buprestidae and a comparative analysis of jewel beetles are presented and the contribution of mt genomes in elucidating phylogenetic relationships within the suborder Polyphaga of Coleoptera is examined.
Journal ArticleDOI
Novel tRNA gene rearrangements in the mitochondrial genome of Camarochiloides weiweii (Hemiptera: Pachynomidae)
TL;DR: Bayesian and maximum likelihood analyses based on sequences of three different mitogenomic datasets recovered the monophyly of Reduvioidea, and the sister relationship between Reduviidae and the remaining Cimicomorpha lineages based on the large-scale sampling.
Journal ArticleDOI
Analysis on the Complete Mitochondrial Genome of Andraca theae (Lepidoptera: Bombycoidea).
TL;DR: The maximum likelihood method and the Bayesian method were used to analyze the phylogenetic relationship among 22 representative bombycoid species with a matrix consisting of the 13 PCGs of the mitogenomes of the 22 species and the results indicated that the bombycid species, including A. theae, clustered into a single clade.
Posted ContentDOI
Selfing is the safest sex for Caenorhabditis tropicalis
Luke M. Noble,Luke M. Noble,John Yuen,Lewis Stevens,Nicolas Moya,Riaad Persaud,Marc Moscatelli,Jacqueline L Jackson,Christian Braendle,Erik C. Andersen,Hannah S. Seidel,Matthew V. Rockman +11 more
TL;DR: Frequent selfing in C. tropicalis may be a strategy to avoid drive-mediated outbreeding depression, andSegregating drivers dramatically reduce fitness, and simulations show that selfing limits their spread.
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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