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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OUP accepted manuscript
TL;DR: In this paper , the characterization of mitochondrial genomes in different decapod crustaceans is described, and the workflows used in these studies are described and compared using open access bioinformatics tools.
Journal ArticleDOI
The complete mitochondrial genomes of the Galápagos iguanas, Amblyrhynchus cristatus and Conolophus subcristatus.
TL;DR: The complete mitochondrial genomes of the marine iguana Amblyrhynchus cristatus and the land iguana Conolophus subcristatus are described and a phylogeny of the Iguanidae is presented, which confirms the sister-group relationship of Galápagos iguanas.
Journal ArticleDOI
Hidden cases of tRNA gene duplication and remolding in mitochondrial genomes of amphipods.
Elena V. Romanova,Yurij S. Bukin,Kirill V. Mikhailov,Kirill V. Mikhailov,Maria D. Logacheva,Maria D. Logacheva,Vladimir V. Aleoshin,Vladimir V. Aleoshin,Dmitry Yu. Sherbakov +8 more
TL;DR: The amphipod-specific tRNA models developed for MiTFi refine existing predictions of tRNA genes in amphipods and reveal additional cases of duplicated t RNA genes overlooked by using less specific Metazoa-wide models.
Journal ArticleDOI
The complete mitogenome of the Emerald Ash Borer (EAB), Agrilus planipennis (Insecta: Coleoptera: Buprestidae).
Jun Duan,Jun Duan,Guoxing Quan,Omprakash Mittapalli,Michel Cusson,Peter J. Krell,Daniel Doucet +6 more
TL;DR: Phylogenetic analysis based on insect mitogenomes indicated that EAB is closely related to other Buprestoidea species, clustering most closely with Chrysochroa fulgidissima.
Journal ArticleDOI
The complete mitochondrial genome of Sarcoptes scabiei var. nyctereutis from the Japanese raccoon dog: Prediction and detection of two transfer RNAs (tRNA-A and tRNA-Y).
Takafumi Ueda,Hiroshi Tarui,Nobuhide Kido,Keitaro Imaizumi,Kenji Hikosaka,Takashi Abe,Daisuke Minegishi,Yoshifumi Tada,Masataka Nakagawa,Sohei Tanaka,Tomoko Omiya,Kouki Morikaku,Minori Kawahara,Takane Kikuchi-Ueda,Teruo Akuta,Yasuo Ono +15 more
TL;DR: The mitochondrial genome structure of S. scabiei is similar to that of Psoroptes cuniculi and Dermatophagoides farinae, and small and unusual tRNA genes seem to be common among acariform mites, while further experimental evidence for their presence is needed.
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.
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.
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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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