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probeBase
Search probeBase for target organisms, probe names, accession numbers, microarrays, target site, references. Match your 16S rRNA sequence(s) against probeBase and find all published probes targeting your sequence(s). View lists of probes (according to probe categories), coverage of group-specific probes, microarrays, references, etc.
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probeCheck
probeCheck provides a freely accessible, central platform for rapid specificity and coverage evaluations of probes and primers against the latest sequence collections of selected phylogenetic and functional marker genes. Using a common user interface a number of established sequence databases can be queried. |
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The ARB Project
16S/18S rRNA database and software environment for sequence data
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rRNA Probes for Protists and Cyanobacteria
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The SILVA rRNA database project
A comprehensive on-line resource for quality checked and aligned ribosomal RNA sequence data, free for academic use. SILVA provides comprehensive, quality checked and regularly updated databases of aligned small (16S/18S, SSU) and large subunit (23S/28S, LSU) ribosomal RNA (rRNA) sequences for all three domains of life (Bacteria, Archaea and Eukarya).
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NCBI
Blast with microbial genomes
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GREENGENES
The greengenes web application provides access to the current and comprehensive 16S rRNA gene sequence alignment for browsing, blasting, probing, and downloading. The data and tools presented by greengenes can assist the researcher in choosing phylogenetically specific probes, interpreting microarray results, and aligning/annotating novel sequences.
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Bioportal
Biportal is a computational resource for bioinformatics and statistical analyses by the University of Oslo. The service is freely available for all academic users. The service uses 300 dedicated cores in a Linux cluster.
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SIMO
The Sapelo Island Microbial rRNA database
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EMBL-EBI
The European Bioinformatics Institute
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