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.
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