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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Characterization of the complete mitochondrial genome of the myrmicine ant Vollenhovia emeryi (Insecta: Hymenoptera: Formicidae)
TL;DR: The myrmicine ant Vollenhovia emeryi is native to East Asia, but has recently become established in North America, and its complete mitochondrial genome has been assembled from Illumina Miseq sequencing data with a good coverage.
Journal ArticleDOI
The complete mitochondrial genome of Histiostoma blomquisti (Acari: Histiostomatidae)
Chih-Chi Lee,John Wang +1 more
TL;DR: Phylogenetic analysis based on the concatenated nucleotide sequence of the 13 protein-coding genes supports Histiostomatid mites forming the basal-most lineage in Astigmata.
Journal ArticleDOI
Shotgun assembly of the complete mitochondrial genome of the neotropical cracker butterfly Hamadryas epinome.
Sébastien Cally,Emeline Lhuillier,Amaia Iribar,Ivonne J. Garzón-Orduña,Eric Coissac,Jérôme Murienne +5 more
TL;DR: The mitochondrial genome of H. epinome was determined to be 15,207 bp long and presents an organization similar to other Ditrysia mitogenomes, including a non-coding poly-AT region of uncertain length.
Journal ArticleDOI
Whole-genome assembly of the coral reef Pearlscale Pygmy Angelfish (Centropyge vrolikii).
TL;DR: This work constructs and compares eight candidate assemblies combining overlapping shotgun read data, mate-pair and Chicago libraries and four different genome assemblers to produce a high-quality draft genome of the iconic coral reef Pearlscale Pygmy Angelfish, Centropyge vrolikii (family Pomacanthidae).
Journal ArticleDOI
Steller's sea cow genome suggests this species began going extinct before the arrival of Paleolithic humans.
Fedor Sharko,Eugenia S. Boulygina,Svetlana V. Tsygankova,N. V. Slobodova,Dmitry A. Alekseev,Anna A. Krasivskaya,Sergey M. Rastorguev,Alexei Tikhonov,Artem V. Nedoluzhko +8 more
TL;DR: In this paper, a nuclear de novo assembled genome of H. gigas with a 25.4× depth coverage was presented, and the results showed that the heterozygosity of the last population of this animal is low and comparable to the last woolly mammoth population that inhabited Wrangel Island 4000 years ago.
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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