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ARB: a software environment for sequence data.
The ARB program package comprises a variety of directly interacting software tools for sequence database maintenance and analysis which are controlled by a common graphical user interface.
Phylogenetic identification and in situ detection of individual microbial cells without cultivation.
Phylogenetic analysis of the retrieved rRNA sequence of an uncultured microorganism reveals its closest culturable relatives and may, together with information on the physicochemical conditions of its natural habitat, facilitate more directed cultivation attempts.
SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB
SILVA (from Latin silva, forest), was implemented to provide a central comprehensive web resource for up to date, quality controlled databases of aligned rRNA sequences from the Bacteria, Archaea and Eukarya domains.
Phylogenetic Oligodeoxynucleotide Probes for the Major Subclasses of Proteobacteria: Problems and Solutions
Uniting the classification of cultured and uncultured bacteria and archaea using 16S rRNA gene sequences
This article proposes rational taxonomic boundaries for high taxa of bacteria and archaea on the basis of 16S rRNA gene sequence identities and suggests a rationale for the circumscription of uncultured taxa that is compatible with the taxonomy of cultured bacteria and Archaea.
The All-Species Living Tree project: a 16S rRNA-based phylogenetic tree of all sequenced type strains.
Notes on the characterization of prokaryote strains for taxonomic purposes.
- B. Tindall, R. Rosselló-Móra, H. Busse, W. Ludwig, P. Kämpfer
- BiologyInternational journal of systematic and…
The purpose of the present article is to outline the key elements in the way that prokaryotes are characterized, with a view to providing an overview of some of the pitfalls commonly encountered in taxonomic papers.
Application of a suite of 16S rRNA-specific oligonucleotide probes designed to investigate bacteria of the phylum cytophaga-flavobacter-bacteroides in the natural environment.
A panel of four 16S rRNA-targeted oligonucleotide probes specific for bacteria of the phylum cytophaga-flavobacter-bacteroides (CFB) were designed and used together with other higher-order probes to analyse the structure and community composition in complex environments.
Sequence heterogeneities of genes encoding 16S rRNAs in Paenibacillus polymyxa detected by temperature gradient gel electrophoresis
The results demonstrate the usefulness of TGGE for the structural analysis of heterogeneous rRNA genes together with their expression, stress problems of the generation of meaningful data for 16S rRNA sequences and probe designs, and might have consequences for evolutionary concepts.
The SILVA and “All-species Living Tree Project (LTP)” taxonomic frameworks
The improvements the SILVA taxonomy has undergone in the last 3 years are described, focusing on the curation process, the various resources used for curation and the comparison of the SILva taxonomy with Greengenes and RDP-II taxonomies.