Josh presentation 4-10-13

2015-01-13

azim58 - Josh presentation 4-10-13

After this presentation I had Josh use his program to find the most
significant epitope in the 108 peptide SMC1fs immunosignature
epitope in 108 SMC1fs peptide immunosignature identified by program of
Josh

some slides that explain how the program made by Josh can find the
predominant epitope in an immunosignature can be found here (note that
these are not the slides for the presentation he gave here on 4-10-13 in
the General Meeting; I think I actually missed this presentation and it
was given at one of the Friday 1pm Array meetings)
"C:\kurt\storage\CIM Research Folder\DR\2013\4-20-13\Linear epitope
finding presentation from Josh\Linear Epitope Finding and Substitution
Analysis on 330k.pptx"

Josh uses Biopython

he didn't look at percentage of biological space the 330k random peptide
array covers. he just looked at how much of random space he covers.

What did he use to make his dendrograms?
Plotting
/home/josh/CIM/Research/
labdata/jaricher/newDecipher/Data for Database/RegExDBSearch/Plot2.py

How to do the HClustering:
http://docs.scipy.org/doc/scipy/reference/cluster.hierarchy.html

Paper on required length of n-mer:
http://www.mcponline.org/content/7/2/247.full
How many n mers are required to resolve a pathogen.
also here: Related papers 2-13-13

How to find how many alignments would align with a protein by chance.
Here's a sketch Josh drew
"C:\kurt\storage\CIM Research Folder\DR\2013\4-10-13\Josh sketch
alignments by random chance 4-10-13.jpg"
Basically, he aligned a particular sequence with 100 random proteins and
established the probability of alignments by chance for that sequence. He
then multiplied that probability by the number of proteins in a
particular pathogen to determine the number of alignments to that
pathogen by chance.
He has a script for this here
/home/josh/CIM/Research/labdata/jaricher/newDecipher/Data for
Database/RandomTest/randEpi.py

Here's an example of running Josh's script to find the predominant main
epitopes in an immunosignature
In [1]: import Data

In [2]: Data.ChipData.fromFileName("..
/")
../Array Results/ ../Proteins_Genomes/
../Bioinformatics_Papers/ ../RandomTest/
../Paper/ ../RegExDBSearch/
../Peptide_Corpus/

In [2]: x=Data.ChipData.fromFileName("../Array Results/First Chip Disease
Dataset/llnl.csv")

In [3]: x.me
x.medianNormalize x.mergeCols

In [3]: x=x.medianNormalize()

In [4]: x.samples
Out[4]:
['BPE',
'BPE',
'BPE',
'BPE',
'BPE',
'BPE',
'BPE',
'BPE',
'BPE',
'BPE',
'BPE',
'BPE',
'Borrelia',
'Borrelia',
'Borrelia',
'Borrelia',
'Borrelia',
'Borrelia',
'Borrelia',
'Borrelia',
'Dengue',
'Dengue',
'Dengue',
'Dengue',
'Dengue',
'Dengue',
'Dengue',
'Dengue',
'Dengue',
'HBV',
'HBV',
'HBV',
'HBV',
'HBV',
'HBV',
'HBV',
'HBV',
'HBV',
'HBV',
'HBV',
'HBV',
'HBV',
'HBV',
'HBV',
'HNP',
'HNP',
'HNP',
'HNP',
'HNP',
'HNP',
'HNP',
'HNP',
'HNP',
'HNP',
'Malaria',
'Malaria',
'Malaria',
'Malaria',
'Malaria',
'Malaria',
'Malaria',
'Malaria',
'Malaria',
'Malaria',
'Malaria',
'Malaria',
'Malaria',
'Normal',
'Normal',
'Normal',
'Normal',
'Normal',
'Normal',
'Normal',
'Normal',
'Normal',
'Normal',
'Normal',
'Normal',
'Normal',
'Normal',
'Normal',
'Normal',
'Normal',
'Normal',
'Normal',
'Normal',
'Normal',
'Normal',
'Normal',
'Normal',
'Normal',
'Normal',
'Normal',
'Normal',
'Normal',
'Normal',
'Normal',
'Normal',
'Syphllis',
'Syphllis',
'Syphllis',
'Syphllis',
'Syphllis',
'Syphllis',
'Syphllis',
'Syphllis',
'WNV',
'WNV',
'WNV',
'WNV',
'WNV',
'WNV',
'WNV',
'WNV',
'WNV',
'WNV',
'WNV',
'WNV',
'WNV',
'WNV',
'WNV',
'WNV',
'WNV',
'WNV',
'WNV',
'WNV',
'WNV']

In [5]: x=x.foldChange("WN",'g')

In [6]: ?x.searchMotifs()
Type: instancemethod
String Form:<bound method ChipData.searchMotifs of <Data.ChipData
instance at 0x3f93290>>
Definition: x.searchMotifs(self, above=4, fuzzy=6, prob='Bon')
Docstring: <no docstring>

In [7]: z=x.searchMotifs(10)
searching 32 peptides

In [8]: z
Out[8]:
[(32,
1,
1.8392572851598359,
[['^.{2,2}DAAPW', [121469], [115566, 121469, 64645],
3.1132551477345425]])]

In [9]:

In [9]: %hst
ERROR: Line magic function `%hst` not found.
In [10]: %his
ERROR: Line magic function `%his` not found.
In [11]:

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