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
The complete mitogenome of the Galaxy Coral, Galaxea fascicularis (Cnidaria: Oculinidae)
TL;DR: The complete mitogenome sequence of Galaxy Coral, Galaxea fascicularis, has been sequenced by next-generation sequencing method and provides essential and important DNA molecular data for further phylogenetic and evolutionary analysis for stony coral.
Dissertation
On the diversification of highly host-specific symbionts: the case of feather mites.
TL;DR: Esta tesis pretende completar este vacio de conocimiento mediante el estudio de los acaros de las plumas de las aves y el modo de transmision y el tipo of interaccion that mantienen con sus hospedadores.
Journal ArticleDOI
EqualTDRL: illustrating equivalent tandem duplication random loss rearrangements
TL;DR: EqualTDRL supports scientists to study the complete set of TDRLs that possibly could have taken place in the evolution of mitochondrial genomes by considering the circularity of the given genomes and certain restrictions on the TDRl rearrangements.
Journal ArticleDOI
CONSULT: accurate contamination removal using locality-sensitive hashing.
TL;DR: ConsULT as mentioned in this paper is a read-matching tool that tests whether k-mers from a query fall within a user-specified distance of the reference dataset using locality-sensitive hashing.
Journal ArticleDOI
The complete mitochondrial genome of Octopus bimaculatus Verrill, 1883 from the Gulf of California
José Francisco Domínguez-Contreras,Adrian Munguia-Vega,Bertha Patricia Ceballos-Vázquez,Francisco Javier García-Rodríguez,Marcial Arellano-Martínez +4 more
TL;DR: A phylogenetic analysis shows a closer relationship between the mitogenomes from O. bimaculatus and O. vulgaris, and contains a VNTR locus not present in the genomes from other octopus species.
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