source: branches/help/HELP_SOURCE/source/rna3d_mapSeqData.hlp @ 18783

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1#Please insert up references in the next lines (line starts with keyword UP)
2UP      arb.hlp
3UP      glossary.hlp
4UP  rna3d_general.hlp
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6#Please insert subtopic references  (line starts with keyword SUB)
7#SUB    subtopic.hlp
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9# Hypertext links in helptext can be added like this: LINK{ref.hlp|http://add|bla@domain}
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11#************* Title of helpfile !! and start of real helpfile ********
12TITLE           Superimposing rRNA sequence data, SAI and probes
13
14OCCURRENCE      In ARB primary structure editor (ARB_EDIT4) -> RNA3D
15
16DESCRIPTION
17
18    SUPERIMPOSING rRNA SEQUENCE DATA
19
20         Any rRNA sequence contained in the multiple sequence alignments of ARB primary
21         structure editor can be overlaid onto the structure of E. coli in the RNA3D
22         window. Desired rRNA sequence to be mapped onto the structure can be selected by
23         the left mouse button in the multiple sequence alignment and the selected rRNA
24         sequence will be instantly mapped onto the master structure.
25
26         The selected rRNA sequence is annotated with mutation (base substitutions),
27         insertion and deletion information at each site as compared to the master
28         sequence (E. coli).
29
30         For the regions where the sequences are aligned without deletion or insertion,
31         direct base substitution (mutation) is applied. Because the C’---C’ distance
32         is essentially the same (~10.2 Å) in all Watson-Crick base pairs (Watson and
33         Crick, 1953), this simple procedure preserves the base pairing and the double
34         helical structure while substituting the bases. Although there do exist the
35         requirement of structural adjustments for non-Watson-Crick base pairs, currently,
36         simple base substitutions are kept because the development of new models to
37         achieve the necessary structural adjustments is out of the scope of the RNA3D
38         tool.
39
40         In the regions where the alignment (of selected rRNA sequence) involves
41         insertions, the respective insertion points to corresponding E. coli base
42         position in the alignment are shown as down arrows in the crystal structure. The
43         number of insertions and the participating nucleotides can also be displayed at
44         the insertion points.
45
46         In the case of regions, where deletions are observed in the alignment
47         corresponding to the master sequence (E. coli), respective sites in the crystal
48         structure are indicated as deleted.
49
50    DISPLAY OPTIONS
51   
52         ENABLE MAPPING:
53
54                Checking this box will enable the mapping or overlaying of any information
55                onto the molecule globally. It is very useful to swiftly switching off
56                mapping information.
57
58         MAP SELECTED SPECIES:
59
60                This check box will enable mapping rRNA sequence data contained in the
61                multiple alignments onto the 3D molecule.
62 
63         DISPLAY BASE DIFFERENCE:
64
65                Enabling this check box will display the substitutions or mutations
66                observed with respect to E.coli sequence onto 16S rRNA 3D structure.
67
68         DISPLAY BASE POSITION:
69
70                Base positions corresponding to the observed substitutions or mutations in
71                the mapped rRNA sequence are displayed by enabling this check box.
72
73         DISPLAY DELETIONS:
74
75                Enabling this check box will display deletions in mapped rRNA sequence
76                with respect to E.coli reference sequence data.
77
78         DISPLAY INSERTIONS:
79
80                Enabling this check box will display insertions in mapped rRNA sequence
81                with respect to E.coli reference sequence data. By checking 'Bases' box,
82                the number of insertions along with the actual bases or residues is
83                displayed at the insertion points.
84
85         DISPLAY MISSING BASES:
86
87                Bases or residues which are presumed to be missing in the rRNA sequence
88                alignments when comparing with the consensus model and/or during manual
89                curation, can be visualized in the 3D structure. Missing bases denoted as
90                dots ('.') in the multiple sequence alignments are mapped onto the rRNA 3D
91                structure as question marks ('?') by enabling this check box. Such missing
92                bases are more often attributed to errors during sequencing.
93
94         Color settings related to mapped sequence data including insertions, deletions,
95         mutations, and missing residues can be changed using 'Color Settings' of the main
96         RNA3D window.
97
98         MAPPING OLIGO-NUCLEOTIDE PROBES:
99
100                The localization of the proposed oligo-nucleotide probe targets can be
101                visualized in customizable background colors with in the rRNA crystal
102                structure. Using the navigation capabilities of RNA3D tool (see
103                “Navigation” section), one can get an idea about the probable binding
104                site of the proposed probe with respect to the structural conformation of
105                rRNA.
106
107                Oligo-nucleotide probes are designed using integrated Probe Design and
108                Probe Match tools of ARB. The selected oligo-nucleotide probe in probe
109                match window is directly mapped onto the rRNA 3D structure by enabling
110                “Map Search Patterns” check box.
111
112         OVERLAYING SEQUENCE ASSOCIATED INFORMATION (SAI):
113
114                Various column statistics like sequence consensus, base frequency,
115                positional variability based on parsimony method and any other user
116                defined column statistics that are performed on the sequence alignments
117                can be readily overlaid onto the 3D structure.
118
119                Once the column statistics are performed, the user can define the color
120                translation table for the chosen SAI in the ARB primary structure editor
121                (see “View | Visualize SAIs” menu). Different colors (up to 10 colors)
122                can be set to the values or characters stored in the SAI to visualize in
123                the molecular structure. The molecule can be re-colored using new settings
124                anytime by clicking the color palate button (using Color Settings in RNA3D
125                window).
126   
127                By enabling the “Map Sequence Associated Information” check box, the
128                transformed data is readily overlaid onto the rRNA 3D structure. Any
129                change in the SAIs and respective color transformations can be reapplied
130                by clicking “refresh” button.
131
132NOTES           None
133
134EXAMPLES        None
135
136WARNINGS        None
137
138BUGS            No bugs known
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