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
Reads0
Chats0
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
More filters
Journal ArticleDOI
Analyses of Mitogenome Sequences Revealed that Asian Citrus Psyllids ( Diaphorina citri ) from California Were Related to Those from Florida
Fengnian Wu,Fengnian Wu,Luci Kumagai,Yijing Cen,Jianchi Chen,Christopher M. Wallis,MaryLou Polek,Hongyan Jiang,Zheng Zheng,Zheng Zheng,Guangwen Liang,Xiaoling Deng +11 more
TL;DR: It is proposed that ACP in California was likely not introduced from China based on the current ACP collection but somewhere in America, however, more studies with ACP samples from around the world are needed.
Journal ArticleDOI
Comparison of whole mitochondrial genome sequences from two clades of the invasive ascidian, Didemnum vexillum.
TL;DR: Differences in functional mitochondrial genes could indicate an increased ability for clade A colonies to tolerate a wider range of environmental temperature and the examination of mitochondrial genotypes, and associated enzyme functioning, across populations may aid in the understanding of thermal tolerance and environmental adaptation.
Journal ArticleDOI
Sequence motifs associated with paternal transmission of mitochondrial DNA in the horse mussel, Modiolus modiolus (Bivalvia: Mytilidae)
TL;DR: This work identifies two evolutionarily Conserved Motifs, CMA and CMB, associated with paternal transmission of mitochondrial DNA, characterized by a conserved purine/pyrimidine pattern, while CMB exhibits a specific 13bp nucleotide string within a stem and loop structure.
Journal ArticleDOI
The complete mitochondrial genome of the big-eye thresher shark, Alopias superciliosus (Chondrichthyes, Alopiidae)
TL;DR: The complete mitochondrial genome of the big-eye thresher shark was sequenced using a polymerase chain reaction (PCR)-based method and the mitochondrial gene arrangement is the same as the one observed in the most vertebrates.
Journal ArticleDOI
The first complete mitochondrial genome of the sand dollar Sinaechinocyamus mai (Echinoidea: Clypeasteroida).
Jih-Pai Lin,Mong-Hsun Tsai,Andreas Kroh,Aaron Trautman,Denis Jacob Machado,Lo-Yu Chang,Robert W. Reid,Kuan-Ting Lin,Omri Bronstein,Shyh-Jye Lee,Daniel Janies +10 more
TL;DR: Phylogenomic analysis based on 34 ingroup taxa belonging to nine orders of the class Echinoidea show congruence between new genetic inference and published trees based on morphologic characters, but also includes some intriguing differences that imply the need for additional investigation.
References
More filters
Journal ArticleDOI
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.
Journal ArticleDOI
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.
Journal ArticleDOI
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.
Related Papers (5)
MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability
Kazutaka Katoh,Daron M. Standley +1 more