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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Using networks to analyze and visualize the distribution of overlapping genes in virus genomes
Laura Muñoz-Baena,Art F. Y. Poon +1 more
TL;DR: A global comparative study of overlapping open reading frames (OvRFs) of 12,609 virus reference genomes in the NCBI database is reported, and a new graph-based representation of the distribution of overlaps among the ORFs of genomes in a given virus family is developed.
Journal ArticleDOI
Aenigmachannidae, a new family of snakehead fishes (Teleostei: Channoidei) from subterranean waters of South India
Ralf Britz,Neelesh Dahanukar,V.K. Anoop,Siby Philip,Brett Clark,Rajeev Raghavan,Lukas Rüber,Lukas Rüber +7 more
TL;DR: The first detailed osteological analysis of Aenigmachanna gollum is provided based on high-resolution nano-CT scans and one cleared and stained specimen of this recently described snakehead fish from subterranean waters of Kerala in South India, indicating that it is a separate lineage of snakeheads and a Gondwanan lineage which has survived break-up of the supercontinent.
Journal ArticleDOI
Pharaoh Cuttlefish, Sepia pharaonis, Genome Reveals Unique Reflectin Camouflage Gene Set
Weiwei Song,Li Ronghua,Li Ronghua,Yun Zhao,Herve Migaud,Herve Migaud,Chunlin Wang,Michaël Bekaert +7 more
TL;DR: A hybrid reference genome of S. pharaonis is produced using a long-read platform (Oxford Nanopore Technologies PromethION) to assemble the genome and short-read, high quality technology (Illumina HiSeq X Ten) to correct for sequencing errors.
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The complete mitochondrial genome of the land snail Cerion incanum (Gastropoda: Stylommatophora) and the phylogenetic relationships of Cerionidae within Panpulmonata
Journal ArticleDOI
The complete mitochondrial genome of Choroterpes (Euthralus) yixingensis (Ephemeroptera: Leptophlebiidae) and its mitochondrial protein-coding gene expression under imidacloprid stress
TL;DR: In this article, the imidacloprid effects on mayfly larvae Choroterpes (Euthralus) yixingensis were investigated and contributed to the phylogenetic status of Ephemeroptera that has always been controversial.
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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