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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Comparative mitochondrial genomics among Spirometra (Cestoda: Diphyllobothriidae) and the molecular phylogeny of related tapeworms
TL;DR: The mt genomes of S. erinaceieuropaei will serve as a useful dataset for studying the genetics and systematics of the species of Spirometra genus in particular and diphyllobothriid tapeworms in general.
Journal ArticleDOI
Adaptive Radiation of the Flukes of the Family Fasciolidae Inferred from Genome-Wide Comparisons of Key Species.
Young Jun Choi,Santiago Fontenla,Peter Fischer,Thanh Hoa Le,Alicia Costábile,David Blair,Paul J. Brindley,José F. Tort,Miguel M. Cabada,Makedonka Mitreva +9 more
TL;DR: Novel insights are provided about the genome evolution of these important pathogens, genomic resources are generated to enable development of improved interventions and diagnosis, and a solid foundation for genomic epidemiology to trace drug resistance and to aid surveillance is laid.
Journal ArticleDOI
Complete mitochondrial and rDNA complex sequences of important vector species of Biomphalaria, obligatory hosts of the human-infecting blood fluke, Schistosoma mansoni.
Si-Ming Zhang,Lijing Bu,Martina R. Laidemitt,Lijun Lu,Martin W. Mutuku,Gerald M. Mkoji,Eric S. Loker +6 more
TL;DR: The authors' analyses reveal that the two taxa inhabiting Lake Victoria, B. sudanica and B. choanomphala, are very similar to one another relative to the similarity either shows to B. pfeifferi or B. glabrata.
Journal ArticleDOI
The complete mitochondrial genome of Paragonimus ohirai (Paragonimidae: Trematoda: Platyhelminthes) and its comparison with P. westermani congeners and other trematodes.
Thanh Hoa Le,Khue Thi Nguyen,Nga Thi Bich Nguyen,Huong Thi Thanh Doan,Takeshi Agatsuma,David Blair +5 more
TL;DR: A phylogenetic tree inferred from concatenated mitochondrial protein sequences of 50 strains encompassing 42 species of trematodes belonging to 14 families identified a monophyletic Paragonimidae in the class Trematoda.
Journal ArticleDOI
Phylogenetic analysis provides insights into the evolution of Asian fireflies and adult bioluminescence.
Xing Chen,Zhiwei Dong,Guichun Liu,Jinwu He,Ruoping Zhao,Wen Wang,Wen Wang,Wen Wang,Yan-Qiong Peng,Xueyan Li +9 more
TL;DR: The data suggest that the common ancestor of Lampyridae possessed adult bioluminescence, with a higher loss rate than gain rate of biolumeinescence during its lineage evolution, and inferred the evolutionary pattern of adult b Bioluminescent in Lampyrids based on the phylogenies of 166 and 144 species.
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.
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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