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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Draft Genome of the Sea Cucumber Holothuria glaberrima, a Model for the Study of Regeneration
Joshua G. Medina-Feliciano,Stacy Pirro,José E. García-Arrarás,Vladimir S. Mashanov,Joseph F. Ryan +4 more
TL;DR: In this article, the first draft genome assembly of H. glaberrima was performed using only short sequencing reads, which resulted in 894 (91.4%) complete and partial genes from 978 genes queried.
Journal ArticleDOI
The mitochondrial genome of the Arizona Snowfly Mesocapnia arizonensis (Plecoptera, Capniidae)
Vasco Elbrecht,Florian Leese +1 more
TL;DR: This is the first partial mitogenome sequence for the stonefly superfamily group Euholognatha and will be useful in future phylogenetic analyses.
Journal ArticleDOI
Episodic positive selection at mitochondrial genome in an introduced biological control agent.
TL;DR: In this article, the authors studied mitochondrial genomes of a world-wide introduced agent, Cryptolaemus montrouzieri, and detected positive selection in complex I genes (ND5 and ND4) against a background of widespread negative selection.
Journal ArticleDOI
Complete mitochondrial genome sequence of fruit-piercing moth Eudocima phalonia (Linnaeus, 1763) (Lepidoptera: Noctuoidea).
Kuppusamy Sivasankaran,Pratheesh Mathew,Sekar Anand,Stanislaus Antony Ceasar,Stanislaus Antony Ceasar,Soosaimanikam Mariapackiam,Savarimuthu Ignacimuthu +6 more
TL;DR: Phylogenetic analysis using PCGs revealed that Superfamily Noctuoidea is a monophyletic group, and the nucleotide composition of the genome is highly A + T biased.
Journal ArticleDOI
Mitochondrial Genomes of Kinorhyncha: trnM Duplication and New Gene Orders within Animals.
Olga V. Popova,Kirill V. Mikhailov,Kirill V. Mikhailov,Mikhail A. Nikitin,Maria D. Logacheva,Maria D. Logacheva,Maria D. Logacheva,Aleksey A. Penin,Aleksey A. Penin,Maria S. Muntyan,Kedrova Os,Nikolai B. Petrov,Yuri V. Panchin,Yuri V. Panchin,Vladimir V. Aleoshin,Vladimir V. Aleoshin +15 more
TL;DR: Gene order analysis reveals that gene arrangement specific of Priapulida may be ancestral for Scalidophora, Ecdysozoa, and even Protostomia.
References
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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.
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