probeBase--an online resource for rRNA-targeted oligonucleotide probes: new features 2007

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 http://www.microbial-ecology.net/probebase. Email correspondence can be addressed to probebase@microbial-ecology.net.

Figure 1

Number of probes per target site and positional variability of the 16/18S rRNA molecule (status July 2006). Positional variability profile of the 16S/18S rRNA in percentage was created using the ARB database “ssu_jan04_corr_opt.arb” (14). Background colors indicate the different fluorescence brightness classes (I, bright to VI, dim) according to the consensus accessibility map of bacterial and archaeal 16S rRNA for FISH probes, established by Behrens et al. (15); uncolored regions were not analyzed.