Module Reduced
source code
Reduced alphabets which lump together several amino-acids into one
letter.
Reduced (redundant or simplified) alphabets are used to represent
protein sequences using an alternative alphabet which lumps together
several amino-acids into one letter, based on physico-chemical traits.
For example, all the aliphatics (I,L,V) are usually quite
interchangeable, so many sequence studies group them into one letter
Examples of reduced alphabets are available in:
http://viscose.ifg.uni-muenster.de/html/alphabets.html
The Murphy tables are from here:
Murphy L.R., Wallqvist A, Levy RM. (2000) Simplified amino acid
alphabets for protein fold recognition and implications for folding.
Protein Eng. 13(3):149-152
Bio.utils.reduce_sequence is used to take a Protein alphabet, and
reduce it using one of the tables here, or a user-defined table.
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murphy_15_tab = { ' A ' : ' A ' , ' C ' : ' C ' , ' D ' : ' D ' , ' E ' : ' E ' , ' F ' : ...
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murphy_15 = Murphy15()
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murphy_10_tab = { ' A ' : ' A ' , ' C ' : ' C ' , ' D ' : ' E ' , ' E ' : ' E ' , ' F ' : ...
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murphy_10 = Murphy10()
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murphy_8_tab = { ' A ' : ' A ' , ' C ' : ' L ' , ' D ' : ' E ' , ' E ' : ' E ' , ' F ' : ' ...
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murphy_8 = Murphy8()
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murphy_4_tab = { ' A ' : ' A ' , ' C ' : ' L ' , ' D ' : ' E ' , ' E ' : ' E ' , ' F ' : ' ...
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murphy_4 = Murphy4()
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hp_model_tab = { ' A ' : ' P ' , ' C ' : ' H ' , ' D ' : ' P ' , ' E ' : ' P ' , ' F ' : ' ...
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pc_5_table = { ' A ' : ' T ' , ' C ' : ' T ' , ' D ' : ' C ' , ' E ' : ' C ' , ' F ' : ' R ' ...
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hp_model = HPModel()
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__package__ = ' Bio.Alphabet '
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murphy_15_tab
- Value:
{ ' A ' : ' A ' ,
' C ' : ' C ' ,
' D ' : ' D ' ,
' E ' : ' E ' ,
' F ' : ' F ' ,
' G ' : ' G ' ,
' H ' : ' H ' ,
' I ' : ' L ' ,
...
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murphy_10_tab
- Value:
{ ' A ' : ' A ' ,
' C ' : ' C ' ,
' D ' : ' E ' ,
' E ' : ' E ' ,
' F ' : ' F ' ,
' G ' : ' G ' ,
' H ' : ' H ' ,
' I ' : ' L ' ,
...
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murphy_8_tab
- Value:
{ ' A ' : ' A ' ,
' C ' : ' L ' ,
' D ' : ' E ' ,
' E ' : ' E ' ,
' F ' : ' F ' ,
' G ' : ' A ' ,
' H ' : ' H ' ,
' I ' : ' L ' ,
...
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murphy_4_tab
- Value:
{ ' A ' : ' A ' ,
' C ' : ' L ' ,
' D ' : ' E ' ,
' E ' : ' E ' ,
' F ' : ' F ' ,
' G ' : ' A ' ,
' H ' : ' E ' ,
' I ' : ' L ' ,
...
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hp_model_tab
- Value:
{ ' A ' : ' P ' ,
' C ' : ' H ' ,
' D ' : ' P ' ,
' E ' : ' P ' ,
' F ' : ' H ' ,
' G ' : ' P ' ,
' H ' : ' P ' ,
' I ' : ' H ' ,
...
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pc_5_table
- Value:
{ ' A ' : ' T ' ,
' C ' : ' T ' ,
' D ' : ' C ' ,
' E ' : ' C ' ,
' F ' : ' R ' ,
' G ' : ' T ' ,
' H ' : ' R ' ,
' I ' : ' A ' ,
...
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