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The Ribosomal Database Project (RDP) is a curated database that offers ribosome data along with related programs and services. The offerings include phylogenetically ordered alignments of ribosomal RNA (rRNA) sequences, derived phylogenetic trees, rRNA secondary structure diagrams and various software packages for handling, analyzing and ...
SILVA [85] is an interdisciplinary project among biologists and computers scientists assembling a complete database of RNA ribosomal (rRNA) sequences of genes, both small (16S, 18S, SSU) and large (23S, 28S, LSU) subunits, which belong to the bacteria, archaea and eukarya domains. These data are freely available for academic and commercial use.
SILVA is a ribosomal RNA database [1] [2] [3] established in collaboration between the Microbial Genomics Group at the Max Planck Institute for Marine Microbiology in Bremen, Germany, the Department of Microbiology at the Technical University Munich, and Ribocon.
EzTaxon-e: database for the identification of prokaryotes based on 16S ribosomal RNA gene sequences; NCBI Taxonomy: a taxonomic database operated by NCBI and concentrating on all taxa for which DNA sequences are available (those sequences are stored by GenBank, another database operated by NCBI).
'The All-Species Living Tree' Project logo ' The All-Species Living Tree' Project is a collaboration between various academic groups/institutes, such as ARB, SILVA rRNA database project, and LPSN, with the aim of assembling a database of 16S rRNA sequences of all validly published species of Bacteria and Archaea. [1]
'The All-Species Living Tree' Project (SILVA LTP) provides a database of 16S rRNA sequences annotated with its own type of taxonomy. Ribosomal database project (RDP) is a similar project. [81] Greengenes is a system that combines the Web of Life phylogeny with 16S data and names from GTDB and LTP, as of version 2. It offers the 16S V4 region ...
For the identification of ribosomal RNA sequences, MG-RAST initiates a BLAT search against a reduced version of the SILVA database. This step allows the system to pinpoint and categorize ribosomal RNA sequences within the dataset, contributing to a more detailed understanding of the biological composition of the analyzed metagenomes or ...
Although it was initially designed for ribosomal RNA data, it can be used for nucleic acid and amino acid sequence data. A central database contains processed (aligned) primary structure data. Additional descriptive data can be stored in database fields assigned to the individual sequences or linked via local or worldwide networks.