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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Characterization of the complete mitochondrial genome of Drawida gisti (Metagynophora, Moniligastridae) and comparison with other Metagynophora species
TL;DR: The complete mitochondrial genome (mitogenome) of Drawida gisti was sequenced and compared with the mitogenomes of other Metagynophora species, andylogenetic analysis suggested that the Moniligastridae contained Drawida, which is a primitive Metaglynophora group.
Journal ArticleDOI
Comprehensive whole genome survey analyses of male and female brown-spotted flathead fish Platycephalus sp.1.
TL;DR: The flathead fish Platycephalus sp.1 is an ecologically and commercially important marine fish in the northwestern Pacific with notable sexual differences in growth and development, yet the genomic data of this species is lacking as discussed by the authors.
Journal ArticleDOI
Genome‐scale data reveal that endemic Poecilia populations from small sulphidic springs display no evidence of inbreeding
Anthony P. Brown,Ryan Greenway,Samuel Morgan,Corey R. Quackenbush,Luca Giordani,Lenin Arias-Rodriguez,Michael Tobler,Joanna L. Kelley +7 more
TL;DR: It is suggested that populations in naturally small habitats may have lower rates of inbreeding and higher genetic diversity than expected, and therefore may be better equipped to handle environmental perturbations than anticipated.
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Molecular phylogeny of ten intertidal hermit crabs of the genus Pagurus inferred from multiple mitochondrial genes, with special emphasis on the evolutionary relationship of Pagurus lanuginosus and Pagurus maculosus.
Zakea Sultana,Akira Asakura,Sonoko Kinjo,Masafumi Nozawa,Masafumi Nozawa,Tomoyuki Nakano,Kazuho Ikeo +6 more
TL;DR: The novel data reported here may provide new perspectives for systematic studies of hermit crabs and provide important information that will facilitate population-level research and identifying intraspecific variation of these non-model, but ecologically important, decapod species.
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Phylogeny and sex chromosome evolution of Palaeognathae
TL;DR: In this article , the evolutionary causes for the different tempos of sex chromosome evolution were investigated in the female genomes of 12 paleognathous species and reconstructed the phylogeny and the evolutionary history of their sex chromosomes.
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.
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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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