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UP	arb.hlp
UP	e4.hlp
UP	pfold.hlp
UP	glossary.hlp

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# Hypertext links in helptext can be added like this: LINK{ref.hlp|http://add|bla@domain}

#************* 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.