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Last update on 12. Oct 2021 .
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Accessibility SAIs

OCCURRENCE  

In databases (e.g. in Silva)

 

DESCRIPTION  

Some arb databases contain accessibility SAIs (like 'E_coli_I_Accessibility').

These SAIs contain information about the FISH probe accessibility to different parts of the molecules of several selected species (Escherichia coli, Pirellula, Metallosphaera sedula, Saccharomyces cerevisiae).

These SAIs contain information about the relative brightness of the fluorescence hybridization signals as determined in [1].

The determined brightness was assigned to six classes of brightness and was encoded into six different characters in the SAIS:

Brightness       Relative          Characters
class            brightness        used in SAIs
I                > 0.8             Ee
II               0.6 - 0.8         Ff
III              0.4 - 0.6         Ii
IV               0.2 - 0.4         Oo
V                0.05- 0.2         Pp
VI               < 0.05            Xx

Different probe target sites often show different signal strengths, even when these sites overlap. That means the probe accessibility depends on the position of the complete probe and its not possible to provide a reasonable accessibility value for single base positions. Therefore the information has been distributed over several separate SAIs, e.g. for Escherichia coli there are five SAIs (E_coli_I_Accessibility, E_coli_II_Accessibility, ..., E_coli_V_Accessibility).

Uppercase characters in the SAI mark the endpoints of single probe sequences, whereas lowercase characters are used for inner positions.

 

NOTES  

The data in the accessibility SAIs is based on the article

[1] In Situ Accessibility of Small-Subunit rRNA of Members of the Domains Bacteria, Archaea, and Eucarya to Cy3-Labeled Oligonucleotide Probes; Sebastian Behrens, Caroline Rühland, João Inácio, Harald Huber, Á. Fonseca, I. Spencer-Martins, Bernhard M. Fuchs, Rudolf Amann; Appl Environ Microbiol. 2003 Mar; 69(3): 1748–1758. doi: 10.1128/AEM.69.3.1748-1758.2003
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC150112/

The integration into ARB and SAI data was described in the article

[2] Graphical representation of ribosomal RNA probe accessibility data using ARB software package; Yadhu Kumar, Ralf Westram, Sebastian Behrens, Bernhard Fuchs, Frank Oliver Glöckner, Rudolf Amann, Harald Meier, Wolfgang Ludwig; BMC Bioinformatics. 2005; 6: 61. Published online 2005 Mar 21. doi: 10.1186/1471-2105-6-61
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1274257/
 

EXAMPLES  

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WARNINGS  

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BUGS  

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