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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The complete mitochondrial genome of the cryptic species (Form II) in kuruma shrimp Marsupenaeus japonicus (Decapoda: Penaeidae).
TL;DR: This study adds a distinct mitogenome of M. japonicus (Form II) from Beibu Bay to provide useful genetic information for future genetic variation identification and genetic diversity evaluation of this economic valuable shrimp.
Journal ArticleDOI
The First Draft Genome of the Plasterer Bee Colletes gigas (Hymenoptera: Colletidae: Colletes)
Qing-Song Zhou,Arong Luo,Feng Zhang,Ze-Qing Niu,Qing-Tao Wu,Mei Xiong,Michael C. Orr,Chao-Dong Zhu +7 more
TL;DR: A high-quality draft genome for C. gigas lays the foundation for insights on the biology and behavior of this species, including its evolutionary history, nesting biology, and interactions with the plant Ca.
Posted ContentDOI
The genome and mRNA transcriptome of the cosmopolitan calanoid copepod Acartia tonsa Dana improve the understanding of copepod genome size evolution
Tue Sparholt Jørgensen,Tue Sparholt Jørgensen,Bent O. Petersen,H. Cecilie B. Petersen,Patrick Denis Browne,Stefan Prost,Stefan Prost,Jonathon H. Stillman,Jonathon H. Stillman,Lars Hestbjerg Hansen,Benni Winding Hansen +10 more
TL;DR: The DNA sequencing-based analyses suggest there is a 14-fold difference in genome size between the six members of Copepoda with available genomic information through NCBI, and the largest copepod genome to date is assembled from PCRfree WGS and mRNA Illumina data.
Journal ArticleDOI
Complete mitochondrial genome of the geniculate calcified red alga, Corallina officinalis (Corallinales, Rhodophyta)
TL;DR: The circular genome of the calcified, geniculate coralline red alga Corallina officinalis (Corallinales) has a gene content consisting of 23 protein-coding genes, 26 transfer RNA genes and two ribosomal RNA genes, with an overall GC content of 30.1%.
Journal ArticleDOI
Resolution of the enigmatic phylogenetic relationship of the critically endangered Western Swamp Tortoise Pseudemydura umbrina (Pleurodira: Chelidae) using a complete mitochondrial genome
TL;DR: Phylogenetic analysis showed that P. umbrina is the monotypic sister lineage to the remaining Australasian Chelidae, a lineage probably dating back to the Cretaceous.
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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