How many times does PQRE occur on array_

2015-01-13

azim58 - How many times does PQRE occur on array?

How many times does "pqre" occur on array?

To answer this question first I need an example gpr file.
I found a gpr file here:
L:\storage\CIM Research Folder\kwhittem\Records in CIM Folder\Dated
Records\3-24-10 SMC1 Blocked 20 Steps Analysis\original gene pix
files\gpr files
This gpr has the peptides for cim10kv2

I will put the files for the rest of this analysis here:
L:\storage\CIM Research Folder\DR\2012\5-2-12\pqre anal

A text file containing just the peptide names is here:
"L:\storage\CIM Research Folder\DR\2012\5-2-12\pqre anal\cim10kv2.txt"

Now I just need to write some code to find the number of occurrences of
the different peptides. I'll find these two different features for each
epitope.
Number of times epitope ("pqre") occurs (some peptides could contain the
epitope more than once):
Number of peptides with epitope:

Here is this information for various epitopes or motifs rather.

PQRE
Number of times epitope "PQRE" occurs: 1
Number of peptides with epitope "PQRE": 1

Number of times epitope "PMRQ" occurs: 4
Number of peptides with epitope "PMRQ": 4

Number of times epitope "PMRE" occurs: 4
Number of peptides with epitope "PMRE": 4

Number of times epitope "PMRD" occurs: 2
Number of peptides with epitope "PMRD": 2

Identity of these PQRE associated peptides

How many times does HE occur?
Number of times epitope "HE" occurs: 942
Number of peptides with epitope "HE": 920

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Code can be found here
"L:\storage\CIM Research Folder\DR\2012\5-2-12\pqre
anal\EpitopeCounter.txt"
and here
"L:\storage\CIM Research Folder\DR\2012\5-2-12\pqre anal\UsefulTools.txt"

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