source: branches/ali/HELP_SOURCE/source/accessibility_sai.hlp

#Please insert up references in the next lines (line starts with keyword UP)
UP      arb.hlp
UP      glossary.hlp
UP      extended.hlp

#Please insert subtopic references  (line starts with keyword SUB)
SUB     visualizeSAI.hlp
SUB     saiProbe.hlp

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#************* Title of helpfile !! and start of real helpfile ********
TITLE           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 RÌhland, 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/

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