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
Preliminary Characterization of Mitochondrial Genome of Melipona scutellaris, a Brazilian Stingless Bee
Manuella Souza Silverio,Vinícius de Rezende Rodovalho,Ana Maria Bonetti,Guilherme Oliveira,Sara Cuadros-Orellana,Carlos Ueira-Vieira,Anderson Rodrigues dos Santos +6 more
TL;DR: The assembly, annotation, and characterization of a draft mitochondrial genome of the Brazilian stingless bee Melipona scutellaris is presented usingMelipona bicolor as a reference organism and it is found that M. cramptoni is the closest species to M. scutelleris.
Journal ArticleDOI
Genomic basis of deep-water adaptation in Arctic Charr (Salvelinus alpinus) morphs.
Tony Kess,J. Brian Dempson,Sarah J. Lehnert,Kara K S Layton,Anthony L. Einfeldt,Paul Bentzen,Sarah J. Salisbury,Amber M. Messmer,Steven Duffy,Daniel E. Ruzzante,Cameron M. Nugent,Moira M. Ferguson,Jong S. Leong,Ben F. Koop,Michael F. O'Connell,Ian Bradbury +15 more
TL;DR: In this article, the authors compare genomic divergence between a deep-water morph adapted to depths of up to 288m and a larger, piscivorous pelagic morph occupying shallower depths using both a SNP array and resequencing of whole nuclear and mitochondrial genomes.
Journal ArticleDOI
Comparative mitochondrial genome analysis and phylogenetic relationship among lepidopteran species.
TL;DR: In this article , the authors integrated 794 mitogenomes consisting of 37 genes and a noncoding control region, which covered 26 lepidopteran superfamilies from newly sequenced and publicly available genomes for comparative genomic and phylogenetic analysis.
Book ChapterDOI
High-Throughput Sequencing of Complete Mitochondrial Genomes.
TL;DR: This chapter outlines methodologies used to sequence, assemble, and annotate mitogenomes of non-model organisms using Illumina sequencing technology, utilizing either long-range PCR amplicons or gDNA as starting template.
Journal ArticleDOI
Characterization of the first mitochondrial genome of a catenulid flatworm: Stenostomum leucops (Platyhelminthes)
TL;DR: The first complete mitochondrial genome of a catenulid, Stenostomum leucops, was characterized and it remains unclear whether the absence of the D arm and loop in trnS1 is a convergence in Catenulida and Neodermata.
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