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#************* Title of helpfile !! and start of real helpfile ********
TITLE           Superimposing rRNA sequence data, SAI and probes

OCCURRENCE      In ARB primary structure editor (ARB_EDIT4) -> RNA3D

DESCRIPTION 

    SUPERIMPOSING rRNA SEQUENCE DATA

         Any rRNA sequence contained in the multiple sequence alignments of ARB primary
         structure editor can be overlaid onto the structure of E. coli in the RNA3D
         window. Desired rRNA sequence to be mapped onto the structure can be selected by
         the left mouse button in the multiple sequence alignment and the selected rRNA
         sequence will be instantly mapped onto the master structure.

         The selected rRNA sequence is annotated with mutation (base substitutions),
         insertion and deletion information at each site as compared to the master
         sequence (E. coli).

         For the regions where the sequences are aligned without deletion or insertion,
         direct base substitution (mutation) is applied. Because the C’---C’ distance
         is essentially the same (~10.2 Å) in all Watson-Crick base pairs (Watson and
         Crick, 1953), this simple procedure preserves the base pairing and the double
         helical structure while substituting the bases. Although there do exist the
         requirement of structural adjustments for non-Watson-Crick base pairs, currently,
         simple base substitutions are kept because the development of new models to
         achieve the necessary structural adjustments is out of the scope of the RNA3D
         tool.

         In the regions where the alignment (of selected rRNA sequence) involves
         insertions, the respective insertion points to corresponding E. coli base
         position in the alignment are shown as down arrows in the crystal structure. The
         number of insertions and the participating nucleotides can also be displayed at
         the insertion points.

         In the case of regions, where deletions are observed in the alignment
         corresponding to the master sequence (E. coli), respective sites in the crystal
         structure are indicated as deleted.

    DISPLAY OPTIONS
    
         ENABLE MAPPING:

                Checking this box will enable the mapping or overlaying of any information
                onto the molecule globally. It is very useful to swiftly switching off
                mapping information.

         MAP SELECTED SPECIES:

                This check box will enable mapping rRNA sequence data contained in the
                multiple alignments onto the 3D molecule.
 
         DISPLAY BASE DIFFERENCE:

                Enabling this check box will display the substitutions or mutations
                observed with respect to E.coli sequence onto 16S rRNA 3D structure.

         DISPLAY BASE POSITION:

                Base positions corresponding to the observed substitutions or mutations in
                the mapped rRNA sequence are displayed by enabling this check box.

         DISPLAY DELETIONS:

                Enabling this check box will display deletions in mapped rRNA sequence
                with respect to E.coli reference sequence data.

         DISPLAY INSERTIONS:

                Enabling this check box will display insertions in mapped rRNA sequence
                with respect to E.coli reference sequence data. By checking 'Bases' box,
                the number of insertions along with the actual bases or residues is
                displayed at the insertion points.

         DISPLAY MISSING BASES:

                Bases or residues which are presumed to be missing in the rRNA sequence
                alignments when comparing with the consensus model and/or during manual
                curation, can be visualized in the 3D structure. Missing bases denoted as
                dots ('.') in the multiple sequence alignments are mapped onto the rRNA 3D
                structure as question marks ('?') by enabling this check box. Such missing
                bases are more often attributed to errors during sequencing.

         Color settings related to mapped sequence data including insertions, deletions,
         mutations, and missing residues can be changed using 'Color Settings' of the main
         RNA3D window.

         MAPPING OLIGO-NUCLEOTIDE PROBES:

                The localization of the proposed oligo-nucleotide probe targets can be
                visualized in customizable background colors with in the rRNA crystal
                structure. Using the navigation capabilities of RNA3D tool (see
                “Navigation” section), one can get an idea about the probable binding
                site of the proposed probe with respect to the structural conformation of
                rRNA.

                Oligo-nucleotide probes are designed using integrated Probe Design and
                Probe Match tools of ARB. The selected oligo-nucleotide probe in probe
                match window is directly mapped onto the rRNA 3D structure by enabling
                “Map Search Patterns” check box.

         OVERLAYING SEQUENCE ASSOCIATED INFORMATION (SAI):

                Various column statistics like sequence consensus, base frequency,
                positional variability based on parsimony method and any other user
                defined column statistics that are performed on the sequence alignments
                can be readily overlaid onto the 3D structure.

                Once the column statistics are performed, the user can define the color
                translation table for the chosen SAI in the ARB primary structure editor
                (see “View | Visualize SAIs” menu). Different colors (up to 10 colors)
                can be set to the values or characters stored in the SAI to visualize in
                the molecular structure. The molecule can be re-colored using new settings
                anytime by clicking the color palate button (using Color Settings in RNA3D
                window).
    
                By enabling the “Map Sequence Associated Information” check box, the
                transformed data is readily overlaid onto the rRNA 3D structure. Any
                change in the SAIs and respective color transformations can be reapplied
                by clicking “refresh” button.

NOTES           None

EXAMPLES        None

WARNINGS        None

BUGS            No bugs known