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 of Macrosteles quadrimaculatus (Matsumura) (Hemiptera: Cicadellidae: Deltocephalinae) with a shared tRNA rearrangement and its phylogenetic implications.
TL;DR: The complete mitochondrial genome of the East Asian species, Macrosteles quadrimaculatus, sequenced and annotated here for the first time, reveals that this species shares the same tRNA rearrangement, suggesting it is a genus-level trait.
Journal ArticleDOI
Comparative mitogenomes of six species in the subfamily Iassinae (Hemiptera: Cicadellidae) and phylogenetic analysis.
TL;DR: Most protein-coding genes in the Iassinae mitogenomes showed typical ATN start codons (ATA/ATT/ATC/ATG) and TAR (TAA/TAG) or an incomplete stop codon T--; ATP8 of all sequenced species showed the start codon TTG.
Posted ContentDOI
Rapid low-cost assembly of the Drosophila melanogaster reference genome using low-coverage, long-read sequencing
Edwin A. Solares,Mahul Chakraborty,Danny E. Miller,Shannon Kalsow,Kate Hall,Anoja Perera,J. J. Emerson,R. Scott Hawley +7 more
TL;DR: This assembly and comparison to the D. melanogaster reference genome demonstrates that high-quality de novo assembly of reference genomes and comprehensive variant discovery using such assemblies are now possible by a single lab for under $1,000 (USD).
Journal ArticleDOI
Phylogenetic perspective on the relationships and evolutionary history of the Acipenseriformes
TL;DR: The Bayesian divergence times showed that the origin time for Acipenseriformes was at 318.0 Mya, which was in good consistent with the paleontological data available and the split time of the Pacific and Atlantic Oceans from the Jurassic to the Cretaceous (Laurasia splits in North America and Eurasia).
Journal ArticleDOI
Unorthodox features in two venerid bivalves with doubly uniparental inheritance of mitochondria.
Charlotte Capt,Karim Bouvet,Davide Guerra,Brent M. Robicheau,Donald T. Stewart,Eric Pante,Sophie Breton +6 more
TL;DR: The complete sex-specific mtDNAs of two recently-discovered DUI species in two families of the order Venerida, Scrobicularia plana (Semelidae) and Limecola balthica (Tellinidae) are presented, indicating that general mitochondrial features are shared among DUI species.
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.
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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.
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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