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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Biochemical and phylogenetic characterization of the wastewater tolerant Chlamydomonas biconvexa Embrapa|LBA40 strain cultivated in palm oil mill effluent.
Patrícia Verdugo Pascoal,Patrícia Verdugo Pascoal,Dágon Manoel Ribeiro,Dágon Manoel Ribeiro,C. R. Cereijo,Hugo Santana,Rodrigo C. Nascimento,Rodrigo C. Nascimento,Andrei Stecca Steindorf,Lorena C. G. Calsing,Eduardo Fernandes Formighieri,Bruno S. A. F. Brasil,Bruno S. A. F. Brasil +12 more
TL;DR: In this article, the microalgal strain Chlamydomonas biconvexa Embrapa|LBA40 was selected among 17 strains tested for growth in POME retrieved from anaerobic ponds of a palm oil industrial plant located within the Amazon rainforest region.
Journal ArticleDOI
Complete mitochondrial genome of the darkling beetle Gonocephalum outreyi (Coleoptera: Tenebrionidae) with phylogenetic implications
TL;DR: The phylogenetic results consistently supported G. outreyi as a member of the family Tenebrionidae, and the monophyly of both Tnebrionoidea and TeneBRionidae were strongly supported.
Journal ArticleDOI
The complete mitochondrial genome of antheraea pernyi strain qing_6 (lepidoptera: Saturniidae).
TL;DR: The complete mitochondrial genome of Antheraea proylei strain In981, a hybrid of Chinese oak silkmoth and Indian oaksilkmoth, is reported, which is the first report on the complete mitochondrial genomes of A.proylei.
Journal ArticleDOI
The mitochondrial genomes of 11 aquatic macroinvertebrate species from Cyprus
Jan-Niklas Macher,Katerina Drakou,Athina Papatheodoulou,Berry van der Hoorn,Marlen I. Vasquez +4 more
TL;DR: The mitochondrial genomes of 11 aquatic macroinvertebrate species from Cyprus are reported and only three species could be provisionally assigned to a binomial species name, highlighting the current lack of molecular references for aquatic macro invertebrates from Cyprus.
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Complete mitogenome of endemic plum-headed parakeet Psittacula cyanocephala - characterization and phylogenetic analysis.
Prateek Dey,Sanjeev Kumar Sharma,Indrani Sarkar,Swapna Devi Ray,P. Pramod,Venkata Hanumat Sastry Kochiganti,Goldin Quadros,Saurabh Singh Rathore,Vikram Singh,Ram Pratap Singh,Ram Pratap Singh +10 more
TL;DR: The Psittacula genus was revealed as paraphyletic nature, containing at least 4 groups of species within the same genus, suggesting its taxonomic reconsideration, and Comparative codon usage analysis indicated the role of natural selection on PsITTacula mitogenomes.
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.
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.
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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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