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

Last change on this file was 19532, checked in by westram, 4 months ago
  • reintegrates 'help' into 'trunk'
    • tweak arb documentation:
      • automatically link
        • ticket references to arb bug tracker (only affects html version).
        • found URLs.
      • page titles
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        • introduce SUBTITLEs (automatically triggered by multi-line titles in source files).
        • increase allowed length (limited by subwindow width).
      • cleanup header sections in all helpfiles.
      • fix and/or update several help files.
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      • build issues:
        • when xml validation fails, next build no longer uses invalid xml ⇒ keeps failing.
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    • moves Tree admin + NDS menu entries to top of menu
  • adds: log:branches/help@18783:19531
File size: 3.3 KB
Line 
1#       main topics:
2UP      arb.hlp
3UP      glossary.hlp
4UP      extended.hlp
5
6#       sub topics:
7SUB     visualizeSAI.hlp
8SUB     saiProbe.hlp
9
10# format described in ../help.readme
11
12
13TITLE           Accessibility SAIs
14
15OCCURRENCE      In databases (e.g. in Silva)
16
17DESCRIPTION     Some arb databases contain accessibility SAIs
18                (like 'E_coli_I_Accessibility').
19
20                These SAIs contain information about the FISH probe accessibility to
21                different parts of the molecules of several selected species (Escherichia
22                coli, Pirellula, Metallosphaera sedula, Saccharomyces cerevisiae).
23
24                These SAIs contain information about the
25                relative brightness of the fluorescence hybridization signals
26                as determined in [1].
27
28                The determined brightness was assigned to six classes of brightness
29                and was encoded into six different characters in the SAIS:
30
31                    Brightness       Relative          Characters
32                    class            brightness        used in SAIs
33
34                    I                > 0.8             Ee
35                    II               0.6 - 0.8         Ff
36                    III              0.4 - 0.6         Ii
37                    IV               0.2 - 0.4         Oo
38                    V                0.05- 0.2         Pp
39                    VI               < 0.05            Xx
40
41                Different probe target sites often show different signal strengths,
42                even when these sites overlap.
43                That means the probe accessibility depends on the position of the complete
44                probe and its not possible to provide a reasonable accessibility value for
45                single base positions.
46                Therefore the information has been distributed over several separate SAIs,
47                e.g. for Escherichia coli there are five SAIs (E_coli_I_Accessibility,
48                E_coli_II_Accessibility, ..., E_coli_V_Accessibility).
49
50                Uppercase characters in the SAI mark the endpoints of single probe sequences,
51                whereas lowercase characters are used for inner positions.
52
53NOTES           The data in the accessibility SAIs is based on the article
54
55                    [1] In Situ Accessibility of Small-Subunit rRNA of Members of the Domains Bacteria, Archaea, and Eucarya to Cy3-Labeled Oligonucleotide Probes;
56                    Sebastian Behrens, Caroline RÃŒhland, João Inácio, Harald Huber, Á. Fonseca, I. Spencer-Martins, Bernhard M. Fuchs, Rudolf Amann;
57                    Appl Environ Microbiol. 2003 Mar; 69(3): 1748–1758. doi: 10.1128/AEM.69.3.1748-1758.2003
58
59                    https://www.ncbi.nlm.nih.gov/pmc/articles/PMC150112/
60
61                The integration into ARB and SAI data was described in the article
62
63                    [2] Graphical representation of ribosomal RNA probe accessibility data using ARB software package;
64                    Yadhu Kumar, Ralf Westram, Sebastian Behrens, Bernhard Fuchs, Frank Oliver Glöckner, Rudolf Amann, Harald Meier, Wolfgang Ludwig;
65                    BMC Bioinformatics. 2005; 6: 61. Published online 2005 Mar 21. doi: 10.1186/1471-2105-6-61
66
67                    https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1274257/
68
69EXAMPLES        None
70
71WARNINGS        None
72
73BUGS            No bugs known
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