PMID- 12520066
OWN - NLM
STAT- MEDLINE
DCOM- 20030314
LR  - 20220311
IS  - 1362-4962 (Electronic)
IS  - 0305-1048 (Print)
IS  - 0305-1048 (Linking)
VI  - 31
IP  - 1
DP  - 2003 Jan 1
TI  - probeBase: an online resource for rRNA-targeted oligonucleotide probes.
PG  - 514-6
AB  - Ribosomal RNA-(rRNA)-targeted oligonucleotide probes are widely used for 
      culture-independent identification of microorganisms in environmental and 
      clinical samples. ProbeBase is a comprehensive database containing more than 700 
      published rRNA-targeted oligonucleotide probe sequences (status August 2002) with 
      supporting bibliographic and biological annotation that can be accessed through 
      the internet at http://www.probebase.net. Each oligonucleotide probe entry 
      contains information on target organisms, target molecule (small- or 
      large-subunit rRNA) and position, G+C content, predicted melting temperature, 
      molecular weight, necessity of competitor probes, and the reference that 
      originally described the oligonucleotide probe, including a link to the 
      respective abstract at PubMed. In addition, probes successfully used for 
      fluorescence in situ hybridization (FISH) are highlighted and the recommended 
      hybridization conditions are listed. ProbeBase also offers difference alignments 
      for 16S rRNA-targeted probes by using the probe match tool of the ARB software 
      and the latest small-subunit rRNA ARB database (release June 2002). The option to 
      directly submit probe sequences to the probe match tool of the Ribosomal Database 
      Project II (RDP-II) further allows one to extract supplementary information on 
      probe specificities. The two main features of probeBase, 'search probeBase' and 
      'find probe set', help researchers to find suitable, published oligonucleotide 
      probes for microorganisms of interest or for rRNA gene sequences submitted by the 
      user. Furthermore, the 'search target site' option provides guidance for the 
      development of new FISH probes.
FAU - Loy, Alexander
AU  - Loy A
AD  - Lehrstuhl fur Mikrobiologie, Technische Universitat Munchen, Am Hochanger 4, 
      D-85350 Freising, Germany.
FAU - Horn, Matthias
AU  - Horn M
FAU - Wagner, Michael
AU  - Wagner M
LA  - eng
PT  - Journal Article
PL  - England
TA  - Nucleic Acids Res
JT  - Nucleic acids research
JID - 0411011
RN  - 0 (Oligonucleotide Probes)
RN  - 0 (RNA Probes)
RN  - 0 (RNA, Ribosomal)
SB  - IM
MH  - Base Sequence
MH  - *Databases, Nucleic Acid
MH  - In Situ Hybridization, Fluorescence
MH  - Internet
MH  - Oligonucleotide Probes/*chemistry
MH  - Phylogeny
MH  - *Prokaryotic Cells
MH  - RNA Probes/*chemistry
MH  - RNA, Ribosomal/*chemistry
MH  - Sequence Alignment
PMC - PMC165463
EDAT- 2003/01/10 04:00
MHDA- 2003/03/15 04:00
PMCR- 2003/01/01
CRDT- 2003/01/10 04:00
PHST- 2003/01/10 04:00 [pubmed]
PHST- 2003/03/15 04:00 [medline]
PHST- 2003/01/10 04:00 [entrez]
PHST- 2003/01/01 00:00 [pmc-release]
AID - gkg016 [pii]
AID - 10.1093/nar/gkg016 [doi]
PST - ppublish
SO  - Nucleic Acids Res. 2003 Jan 1;31(1):514-6. doi: 10.1093/nar/gkg016.