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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First mitogenome for the tribe Saccharosydnini (Hemiptera: Delphacidae: Delphacinae) and the phylogeny of three predominant rice planthoppers
Yi-Xin Huang,Dao-Zheng Qin +1 more
TL;DR: The mitochondrial genome of Saccharosydne procerus (Matsumura) is the first sequenced in the tribe SaccharOSydnini and the existence of purifying selection was indicated by the rate of nonsynonymous and synonymous substitutions.
Journal ArticleDOI
The Complete Mitochondrial Genome Sequence of Bactericera cockerelli and Comparison with Three Other Psylloidea Species.
Fengnian Wu,Fengnian Wu,Yijing Cen,Christopher M. Wallis,John T. Trumble,Sean M. Prager,Ray Yokomi,Zheng Zheng,Zheng Zheng,Xiaoling Deng,Jianchi Chen,Guangwen Liang +11 more
TL;DR: This report provides the first complete B. cockerelli mitogenome sequence as determined by next generation sequencing technology (Illumina MiSeq) and revealed differences between and among the insect families, in particular a unique region that can be folded into three stem-loop secondary structures present only within the B.
Posted ContentDOI
Draft Genome of the Sea Cucumber Holothuria glaberrima, a model for the study of regeneration
Joshua G. Medina-Feliciano,Stacy Pirro,José E. García-Arrarás,Vladimir S. Mashanov,Joseph F. Ryan +4 more
TL;DR: The first draft genome assembly of H. glaberrima is reported and the usefulness of the genome is demonstrated, including the melanotransferrin (Mtf) gene family, which have a potential role in regeneration of the sea cucumber intestine.
Journal ArticleDOI
Complete mitochondrial genome of the European Grapevine moth (EGVM) Lobesia botrana (Lepidoptera: Tortricidae)
TL;DR: The circular mitochondrial genome of L. botrana represents a valuable molecular resource for developing effective DNA identification tools for biosecurity purposes and will contribute to better understanding of its evolutionary and population genetics.
Journal ArticleDOI
An RNA-based approach to sequence the mitogenome of Hypoptopoma incognitum (Siluriformes: Loricariidae).
Daniel A. Moreira,Maithê G. P. Magalhães,Paula C. C. de Andrade,Carolina Furtado,Adalberto Luis Val,Thiago E.M. Parente +5 more
TL;DR: An innovative RNA-based approach was used to assemble the complete mitogenome of H. incognitum, a fish of the fifth most species-rich family of vertebrates and abundant in rivers from the Brazilian Amazon.
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.
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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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