PMID- 15777482
OWN - NLM
STAT- MEDLINE
DCOM- 20060126
LR  - 20181113
IS  - 1471-2105 (Electronic)
IS  - 1471-2105 (Linking)
VI  - 6
DP  - 2005 Mar 21
TI  - Graphical representation of ribosomal RNA probe accessibility data using ARB 
      software package.
PG  - 61
AB  - BACKGROUND: Taxon specific hybridization probes in combination with a variety of 
      commonly used hybridization formats nowadays are standard tools in microbial 
      identification. A frequently applied technology, fluorescence in situ 
      hybridization (FISH), besides single cell identification, allows the localization 
      and functional studies of the microbial community composition. Careful in silico 
      design and evaluation of potential oligonucleotide probe targets is therefore 
      crucial for performing successful hybridization experiments. RESULTS: The PROBE 
      Design tools of the ARB software package take into consideration several criteria 
      such as number, position and quality of diagnostic sequence differences while 
      designing oligonucleotide probes. Additionally, new visualization tools were 
      developed to enable the user to easily examine further sequence associated 
      criteria such as higher order structure, conservation, G+C content, 
      transition-transversion profiles and in situ target accessibility patterns. The 
      different types of sequence associated information (SAI) can be visualized by 
      user defined background colors within the ARB primary and secondary structure 
      editors as well as in the PROBE Match tool. CONCLUSION: Using this tool, in 
      silico probe design and evaluation can be performed with respect to in situ probe 
      accessibility data. The evaluation of proposed probe targets with respect to 
      higher-order rRNA structure is of importance for successful design and 
      performance of in situ hybridization experiments. The entire ARB software package 
      along with the probe accessibility data is available from the ARB home page 
      http://www.arb-home.de
FAU - Kumar, Yadhu
AU  - Kumar Y
AD  - Lehrstuhl fur Mikrobiologie, Technische Universitat Munchen, D-85350 Freising, 
      Germany. yadhu@mikro.biologie.tu-muenchen.de
FAU - Westram, Ralf
AU  - Westram R
FAU - Behrens, Sebastian
AU  - Behrens S
FAU - Fuchs, Bernhard
AU  - Fuchs B
FAU - Glockner, Frank Oliver
AU  - Glockner FO
FAU - Amann, Rudolf
AU  - Amann R
FAU - Meier, Harald
AU  - Meier H
FAU - Ludwig, Wolfgang
AU  - Ludwig W
LA  - eng
PT  - Journal Article
PT  - Research Support, Non-U.S. Gov't
DEP - 20050321
PL  - England
TA  - BMC Bioinformatics
JT  - BMC bioinformatics
JID - 100965194
RN  - 0 (Bacterial Proteins)
RN  - 0 (DNA Primers)
RN  - 0 (Oligonucleotide Probes)
RN  - 0 (RNA Probes)
RN  - 0 (RNA, Bacterial)
RN  - 0 (RNA, Ribosomal)
RN  - 63231-63-0 (RNA)
SB  - IM
MH  - Algorithms
MH  - Bacterial Proteins/*genetics
MH  - Computer Graphics
MH  - Computer Simulation
MH  - DNA Primers
MH  - Data Interpretation, Statistical
MH  - Databases, Genetic
MH  - Databases, Nucleic Acid
MH  - Genes, Bacterial/*genetics
MH  - In Situ Hybridization
MH  - In Situ Hybridization, Fluorescence/*methods
MH  - Internet
MH  - Nucleic Acid Hybridization
MH  - Oligonucleotide Probes/*chemistry
MH  - Phylogeny
MH  - Programming Languages
MH  - RNA
MH  - RNA Probes/chemistry
MH  - RNA, Bacterial
MH  - RNA, Ribosomal/*analysis/chemistry
MH  - Ribosomes
MH  - Sequence Alignment
MH  - Sequence Analysis, Protein
MH  - Software
MH  - Software Design
MH  - User-Computer Interface
PMC - PMC1274257
EDAT- 2005/03/22 09:00
MHDA- 2006/01/27 09:00
PMCR- 2005/03/21
CRDT- 2005/03/22 09:00
PHST- 2004/10/12 00:00 [received]
PHST- 2005/03/21 00:00 [accepted]
PHST- 2005/03/22 09:00 [pubmed]
PHST- 2006/01/27 09:00 [medline]
PHST- 2005/03/22 09:00 [entrez]
PHST- 2005/03/21 00:00 [pmc-release]
AID - 1471-2105-6-61 [pii]
AID - 10.1186/1471-2105-6-61 [doi]
PST - epublish
SO  - BMC Bioinformatics. 2005 Mar 21;6:61. doi: 10.1186/1471-2105-6-61.