probeCheck--a central resource for evaluating oligonucleotide probe coverage and specificity - PubMed (original) (raw)

probeCheck--a central resource for evaluating oligonucleotide probe coverage and specificity

Alexander Loy et al. Environ Microbiol. 2008 Oct.

Free PMC article

Abstract

The web server probeCheck, freely accessible at http://www.microbial-ecology.net/probecheck, provides a pivotal forum for rapid specificity and coverage evaluations of probes and primers against selected databases of phylogenetic and functional marker genes. Currently, 24 widely used sequence collections including the Ribosomal Database Project (RDP) II, Greengenes, SILVA and the Functional Gene Pipeline/Repository can be queried. For this purpose, probeCheck integrates a new online version of the popular ARB probe match tool with free energy (DeltaG) calculations for each perfectly matched and mismatched probe-target hybrid, allowing assessment of the theoretical binding stabilities of oligo-target and non-target hybrids. For each output sequence, the accession number, the GenBank taxonomy and a link to the respective entry at GenBank, EMBL and, if applicable, the query database are displayed. Filtering options allow customizing results on the output page. In addition, probeCheck is linked with probe match tools of RDP II and Greengenes, NCBI blast, the Oligonucleotide Properties Calculator, the two-state folding tool of the DINAMelt server and the rRNA-targeted probe database probeBase. Taken together, these features provide a multifunctional platform with maximal flexibility for the user in the choice of databases and options for the evaluation of published and newly developed probes and primers.

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Figures

Fig. 1

Fig. 1

probeCheck screen shot. (Upper panel) An example of the probeCheck output using the _Desulfomicrobium_-specific 16S rRNA-targeted probe DSM213 (probeBase Accession No. pB-00507) (Lücker et al., 2007) as query sequence and the 16S/18S rRNA sequence database from SILVA. (Lower panel) Same as above, except that the results were filtered to exclude environmental sequences by excluding hits containing the term ‘uncultured’ in the species/sequence name.

References

    1. Ashelford KE, Weightman AJ, Fry JC. PRIMROSE: a computer program for generating and estimating the phylogenetic range of 16S rRNA oligonucleotide probes and primers in conjunction with the RDP-II database. Nucleic Acids Res. 2002;30:3481–3489. - PMC - PubMed
    1. Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Wheeler DL. GenBank. Nucleic Acids Res. 2007;35:D21–D25. - PMC - PubMed
    1. Brosius J, Dull TL, Sleeter DD, Noller HF. Gene organization and primary structure of a ribosomal operon from Escherichia coli. J Mol Biol. 1981;148:107–127. - PubMed
    1. Cole JR, Chai B, Farris RJ, Wang Q, Kulam-Syed-Mohideen AS, McGarrell DM, et al. The ribosomal database project (RDP-II): introducing myRDP space and quality controlled public data. Nucleic Acids Res. 2007;35:D169–D172. - PMC - PubMed
    1. Daims H, Stoecker K, Wagner M. Fluorescence in situ hybridization for the detection of prokaryotes. In: Osborn AM, Smith CJ, editors. Advanced Methods in Molecular Microbial Ecology. Abingdon, UK: BIOS Scientific Publishers; 2005. pp. 213–239.

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