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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Six complete mitochondrial genomes of mayflies from three genera of Ephemerellidae (Insecta: Ephemeroptera) with inversion and translocation of trnI rearrangement and their phylogenetic relationships.
TL;DR: Among the phylogenetic relationship of the Ephemeroptera, the monophyly of almost all families except Siphlonuridae was supported by BI and ML analyses and indicated that Ephemerellidae was the sister clade to Vietnamellidae whereas Teloganellidae was not a sisterClade of Ephemrellidae and Viet Namellidae.
Journal ArticleDOI
The First Mitochondrial Genome of the Sepsid Fly Nemopoda mamaevi Ozerov, 1997 (Diptera: Sciomyzoidea: Sepsidae), with Mitochondrial Genome Phylogeny of Cyclorrhapha
TL;DR: Ozerov et al. as discussed by the authors sequenced the first complete mt genome of the sepsid fly Nemopoda mamaevi Ozerov, 1997, which is typical of Diptera, containing all 37 genes usually present in bilaterian animals.
Journal ArticleDOI
Comparative mitogenomics, phylogeny and evolutionary history of Leptogorgia (Gorgoniidae).
Angelo Poliseno,Christian Feregrino,Stéphane Sartoretto,Didier Aurelle,Gert Wörheide,Catherine S. McFadden,Sergio Vargas +6 more
TL;DR: The phylogenetic analyses using complete mitogenomes and an extended mtMutS dataset recovered Leptogorgia as polyphyletic, and the species considered were split into two defined groups corresponding to different geographic regions, namely the eastern Pacific and the Atlantic-Mediterranean.
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Comparative analysis of the mitochondrial genomes of oriental spittlebug trible Cosmoscartini: insights into the relationships among closely related taxa.
TL;DR: It is indicated that knowledge of mitogenomes can be effectively used to resolve phylogenetic relationships at low taxonomic levels and represents the first detailed comparative genomic and phylogenetic analyses within Cercopidae.
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An alpine grasshopper radiation older than the mountains, on Kā Tiritiri o te Moana (Southern Alps) of Aotearoa (New Zealand).
TL;DR: It is inferred that the most recent common ancestor of New Zealand and Tasmanian grasshoppers existed about 20 million years ago, suggesting alpine species diversification occurred in New Zealand well before the Southern Alps were formed by the mountain building events of the Kaikoura Orogeny 2-5 Mya.
References
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Journal ArticleDOI
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.
Journal ArticleDOI
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.
Journal ArticleDOI
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.
Journal ArticleDOI
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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