probeBase--an online resource for rRNA-targeted oligonucleotide probes: new features 2007
Top Cited Papers
Open Access
- 11 November 2006
- journal article
- research article
- Published by Oxford University Press (OUP) in Nucleic Acids Research
- Vol. 35 (Database) , D800-D804
- https://doi.org/10.1093/nar/gkl856
Abstract
ProbeBase is a curated database of annotated rRNA-targeted oligonucleotide probes and supporting information. Rapid access to probe, microarray and reference data is achieved by powerful search tools and via different lists that are based on selected categories such as functional or taxonomic properties of the target organism(s) or the hybridization format (fluorescence in situ hybridization or microarray) in which the probes were applied. Additional information on probe coverage and specificity is available through direct submissions of probe sequences from probeBase to RDP-II and Greengenes, two major rRNA sequence databases. A freely editable user comments field for each probe entry allows any user to add, modify or remove information or to report errors in real-time. probeBase entries increased from 700 to more than 1200 during the past three years. Several options for submission of single probes or entire probe sets, even prior to publication of newly developed probes, should further contribute to keeping probeBase an up-to-date and useful resource. probeBase is freely accessible at Author Webpage. Email correspondence can be addressed to probebase@microbial-ecology.net.Keywords
This publication has 25 references indexed in Scilit:
- Greengenes, a Chimera-Checked 16S rRNA Gene Database and Workbench Compatible with ARBApplied and Environmental Microbiology, 2006
- Linking microbial community structure with function: fluorescence in situ hybridization-microautoradiography and isotope arraysCurrent Opinion in Biotechnology, 2006
- Making All Parts of the 16S rRNA of Escherichia coli Accessible In Situ to Single DNA OligonucleotidesApplied and Environmental Microbiology, 2006
- daime, a novel image analysis program for microbial ecology and biofilm researchEnvironmental Microbiology, 2005
- 16S rRNA Gene-Based Oligonucleotide Microarray for Environmental Monitoring of the Betaproteobacterial Order “Rhodocyclales”Applied and Environmental Microbiology, 2005
- Mechanistic Approach to the Problem of Hybridization Efficiency in Fluorescent In Situ HybridizationApplied and Environmental Microbiology, 2004
- In Situ Accessibility of Small-Subunit rRNA of Members of the Domains Bacteria , Archaea , and Eucarya to Cy3-Labeled Oligonucleotide ProbesApplied and Environmental Microbiology, 2003
- Detection and Differentiation of Chlamydiae by Fluorescence In Situ HybridizationApplied and Environmental Microbiology, 2002
- Investigation of Candidate Division TM7, a Recently Recognized Major Lineage of the Domain Bacteria with No Known Pure-Culture RepresentativesApplied and Environmental Microbiology, 2001
- Monitoring a widespread bacterial group: in situ detection of planctomycetes with 16S rRNA-targeted probesMicrobiology, 1998