Journal ArticleDOI
Accurate and universal delineation of prokaryotic species
TLDR
The specI (species identification tool) as mentioned in this paper ) is a method to group organisms into species clusters based on 40 universal, single-copy phylogenetic marker genes, applied to 3,496 prokaryotic genomes, specI identified 1,753 species clusters.Abstract:
The exponentially increasing number of sequenced genomes necessitates fast, accurate, universally applicable and automated approaches for the delineation of prokaryotic species. We developed specI (species identification tool; http://www.bork.embl.de/software/specI/), a method to group organisms into species clusters based on 40 universal, single-copy phylogenetic marker genes. Applied to 3,496 prokaryotic genomes, specI identified 1,753 species clusters. Of 314 discrepancies with a widely used taxonomic classification, >62% were resolved by literature support.read more
Citations
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Journal ArticleDOI
Draft Genome Sequences of Two Potentially Novel Bacillus Isolates from Backyard and Commercial Chicken Gastrointestinal Tracts.
TL;DR: The draft genome sequences of two Bacillus strains isolated in Pomona, California, from the gastrointestinal (GI) tract of backyard and commercial broiler chickens appear to represent novel species.
Posted ContentDOI
Analysis of metagenome-assembled genomes from the mouse gut microbiota reveals distinctive strain-level characteristics
Shenghui Li,Shenghui Li,Siyi Zhang,Bo Li,Shanshan Sha,Jian Kang,Peng Li,Aiqin Zhang,Qianru Ji,Qing-Bo Lv,Xiao-Xuan Zhang,Hongbo Ni,Xiuyan Han,Miao Xu,Guangyang Wang,Wenzhe Zhang,Yuanyuan Sun,Roujia Xu,Yi Xin,Qiulong Yan,Yufang Ma +20 more
TL;DR: A unique ecosystem in the gut of laboratorial mice that obviously differed with the human gut flora at the strain level was highlighted, which may be beneficial to researches based on laboratorial mouse models.
Book ChapterDOI
Molecular Tools in Microbial Diversity: Functional Assessment Tool for Genomes and Metagenomes, MAPLE System
TL;DR: This chapter provides the methodology for functional genomics and metagenomics to reveal not only species diversity but also the functional diversity of individual microbes and whole microbial communities.
Journal ArticleDOI
Characterization and genomic analysis of two novel psychrotolerant Acidithiobacillus ferrooxidans strains from polar and subpolar environments
Claudia M. Muñoz-Villagrán,Jonnathan Grossolli-Gálvez,Javiera Acevedo-Arbunic,Ximena Valenzuela,Alonso Ferrer,Beatriz Díez,Gloria Levicán +6 more
TL;DR: Cold-adapted cultures of the At.
References
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Journal ArticleDOI
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs.
Stephen F. Altschul,Thomas L. Madden,Alejandro A. Schäffer,Jinghui Zhang,Zheng Zhang,Webb Miller,David J. Lipman +6 more
TL;DR: A new criterion for triggering the extension of word hits, combined with a new heuristic for generating gapped alignments, yields a gapped BLAST program that runs at approximately three times the speed of the original.
Journal ArticleDOI
Search and clustering orders of magnitude faster than BLAST
TL;DR: UCLUST is a new clustering method that exploits USEARCH to assign sequences to clusters and offers several advantages over the widely used program CD-HIT, including higher speed, lower memory use, improved sensitivity, clustering at lower identities and classification of much larger datasets.
Book
Bergey's Manual of Systematic Bacteriology
TL;DR: BCL3 and Sheehy cite Bergey's manual of determinative bacteriology of which systematic bacteriology, first edition, is an expansion.
Journal ArticleDOI
RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models
TL;DR: UNLABELLED RAxML-VI-HPC (randomized axelerated maximum likelihood for high performance computing) is a sequential and parallel program for inference of large phylogenies with maximum likelihood (ML) that has been used to compute ML trees on two of the largest alignments to date.
Journal ArticleDOI
Improved tools for biological sequence comparison.
TL;DR: Three computer programs for comparisons of protein and DNA sequences can be used to search sequence data bases, evaluate similarity scores, and identify periodic structures based on local sequence similarity.
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