source: tags/ms_r16q4/HELP_SOURCE/oldhelp/pfold_props.hlp

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#************* Title of helpfile !! and start of real helpfile ********
TITLE           Protein Match Settings

OCCURRENCE      ARB_EDIT4/Properties/Protein Match Settings

DESCRIPTION

        In the 'Protein Match Settings' window the protein structure match
        computation can be configured. The settings are described in the following
        section.

SECTION Configuration

        Show protein structure match: Toggle display of protein match symbols
        
        Selected Protein Structure SAI: The protein secondary structure SAI used as
        reference for match computation. The default is 'PFOLD'.
                
        Filter SAI names for: Via a filter the SAIs shown in the option menu can be
        narrowed down to a selection of SAIs whose names contain the specified
        string. This is useful for a great number of SAIs to quickly find the
        one that should be used. Default is 'pfold'.
                
        Match Method: The used method for protein structure match computation.
        Default is 'Secondary Structure <-> Sequence' which is most probable the
        method of choice. Details on the different methods can be found below in
        section 'Description of Match Methods'.
                
        Match Symbols (only relevant for the match method 'Secondary Structure <->
        Sequence'): Ten symbols that represent the match quality ranging from
        0 - 100% in steps of 10%. Take care to enter exactly ten symbols.
        Note that spaces (' ') are symbols, too.

        Pair definitions (only relevant for the match methods 'Secondary Structure
        <-> Secondary Structure' and 'Secondary Structure <-> Sequence (Full
        Prediction)'). Each line contains two textfields:
        - The left textfield contains one or more amino acid pairs. Each
          pair contains two characters (amino acids, gaps-characters, ...).
          Pairs are separated by spaces (' ').
        - The right textfield contains the match symbol used for each
          of the specified pairs.

SECTION Description of Match Methods

        Match Method 'Secondary Structure <-> Secondary Structure'
        
                Use this method if you want to compare protein secondary structures
                only. The characters representing species secondary structures are
                compared one by one with the ones of the selected secondary structure
                SAI using the pair definitions and the defined match symbols. If
                undefined pairs are encountered the 'Unknown_match' symbol is
                displayed.
        
        Match Method 'Secondary Structure <-> Sequence'
        
                Species amino acid sequences are compared with the selected secondary
                structure SAI by taking cohesive parts of the structure - gaps in the
                alignment are skipped - and computing values from 0 - 100% (in steps
                of 10%) for the match quality which are mapped to the defined match
                symbols. The whole part is marked with that symbol. Note that bends
                ('S') are assumed to fit everywhere (=> best match symbol), and if a
                structure is encountered but no corresponding amino acid the worst
                match symbol is displayed.
        
        Match Method 'Secondary Structure <-> Sequence (Full Prediction)'
        
                Species amino acid sequences are compared with the selected secondary
                structure SAI using a full prediction of secondary structures from
                their sequences (via the Chou-Fasman algorithm) and comparing the
                characters one by one with the reference structure SAI. Note that not
                the structure summaries are used for comparison, but individually
                predicted alpha-helices ('H'), beta-sheets ('E') and beta-turns ('T').
                The pair definitions are searched in ascending order, i.e. good
                matches first, then the worse ones. If a match is found the
                corresponding match symbol is displayed. Note that if a structure is
                encountered but no corresponding amino acid the worst match symbol is
                displayed.

NOTES

        - The menu entry 'Properties -> Protein Match Settings' is only shown for
          protein alignments ('Alignment Information -> <Type of Sequences>: pro',
          see LINK{ad_align.hlp}).
        - The match computation for sequences and secondary structures is based on
          the Chou-Fasman algorithm or adaptions to it. See LINK{pfold.hlp} for
          explanation and reference.

SECTION TODO

        The settings window should only show the fields that are relevant
        for the current match method.

EXAMPLES        None

WARNINGS

        !!! The match computation can only give a rough overview if a given amino
        acid sequence matches a certain secondary structure. Do not fully rely on
        it but use it as hints for aligning your amino acid sequences. !!!

        !!! The match method 'Secondary Structure <-> Sequence (Full Prediction)' is
        experimental. It is probably not very reliable and requires a lot of
        computation. Thus, it should not be used for a large number of species loaded
        in the editor. !!!

BUGS

        The editor might be unstable and can crash if sequences are not formatted.