This is a library to evaluate an aminoacid sequence and determine an amphipathic index for each alpha helix or beta sheet.
Project description
amphipathic
This is a library to evaluate an aminoacid sequence and determine an amphipathic index for each alpha helix or beta sheet.
Requirements
If you want to use this library on any GNU/Linux or OSX system you just need to execute:
$ pip install amphipathic
If you want to collaborate with this library, you should download the github repository and execute:
$ make deploy
Testing
To test all the project you should use the command:
$ make test
Example
This library can analyze an aminoacid sequence and gives a list of secondary structures with the respective index:
import amphipathic
resume = amphipathic.index('NLYIQWLKDGGPSSGRPPPS')
print resume
And the result should be:
[[
{'end': 2,
'begin': 0,
'type': u'c',
'seq': 'nl',
'amphipathic': {'index': 7.572935321054872e-05, 'mean': 2.6}},
{'end': 5,
'begin': 2,
'type': u'e',
'seq': 'yiq',
'amphipathic': {'index': 1.4312912272216411, 'mean': 1.7299999999999998}},
{'end': 18,
'begin': 5,
'type': u'c',
'seq': 'wlkdggpssgrpp',
'amphipathic': {'index': 0.002511560979331271, 'mean': -0.43}},
{'end': 20,
'begin': 18,
'type': u'e',
'seq': 'ps',
'amphipathic': {'index': 1.6242872515167746, 'mean': -1.34}}
]]
It also accept a nucleotide sequence to perform the same analysis:
import amphipathic
resume = amphipathic.index('cgcgtccttggagcaatgcagttcaagaccaagaatcgaattgaacctgt')
print resume
And the output:
[[
{'end': 12,
'begin': 0,
'type': u'c',
'seq': 'rvlgamqfktkn',
'amphipathic': {'index': 0.007560225956225585, 'mean': 0.7825000000000001}},
{'end': 15,
'begin': 12,
'type': u'e',
'seq': 'rie',
'amphipathic': {'index': 1.6297837670649824, 'mean': 1.4599999999999997}},
{'end': 16,
'begin': 15,
'type': u'c',
'seq': 'p',
'amphipathic': {'index': 0.0, 'mean': -2.23}}
]]
Last, it also accept a polyprotein sequence. When working with aminoacid it detect the '*' character as a stop signal:
import amphipathic
resume = amphipathic.index('NLYIQWLKDG*GPSSGRPPPS')
print resume
Questions?
If you want to develope with us or have questions about this library, please file an issue in this repository so some of the project managers can get back to you. Please check the existing (and closed) issues to make sure your issue hasn't already been addressed.
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