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
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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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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