Details
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Type: New Feature
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Status: Open
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Priority: Minor
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Resolution: Unresolved
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Affects Version/s: 2.7_gsoc11, 2.8
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Fix Version/s: 2.7_gsoc11
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Component/s: gui
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Labels:None
Description
The existing 'consensus' sequence logo is calculated using 'per column' symbol frequencies. This idea can be extended to pairwise sequence logos, where for an alignment like:
>sa
CCCGU
>sb
UUUGC
and secondary structure:
((.))
The logo at each position reflects the percentage of each type of base pair:
Position 1: [ CU ] 50%; [UC] 50%.
Position 2: [ UG ] 50%; [ CG ] 50%.
Position 4 and 5 would give the inverse view, ie:
Position 1: [ UC ] 50%; [ CU ] 50%.
Position 2: [ GU ] 50%; [ GC ] 50%.