User: Girolamo
Girolamo • 140
- Reputation:
- 140
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- Location:
- Italia
- Last seen:
- 2 years, 1 month ago
- Joined:
- 7 years, 10 months ago
- Email:
- g***************@gmail.com
Hello i'm studing bioinformatic I work on parallel computing applied to bioinformatics, in particular I work on graph matching
Posts by Girolamo
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Answer:
A: Huge matrix memory issue
... I assume you have a sparse matrix
you could represent the matrix as a combination of three arrays
http://btechsmartclass.com/DS/U1_T14.html
another possibility is to use shelve
https://docs.python.org/2/library/shelve.html
...
written 2.2 years ago by
Girolamo • 140
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... you can also have a look to panther
http://pantherdb.org/
...
written 2.4 years ago by
Girolamo • 140
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A: Motif discovery using MEME
... Is the difference in terms of e-values huge?
As far as I remember, the background is calculated by shuffling the sequences in the input, hence you can have a slight difference
Are the versions(online and offline) the same? ...
written 2.5 years ago by
Girolamo • 140
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Comment:
C: PIN or PPI Network Construction
... If I remember correctly, string (http://string-db.org/) already adopts this approach. ...
written 2.5 years ago by
Girolamo • 140
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... 1 and 2) these two questions are correlated. This affects the reliability of your network.
I would remove text mining and the other options, and leave only those interaction experimentally validated with a threshold > 0.700.
3) do you want to do it routinely for all the 110 proteins? this could ...
written 2.8 years ago by
Girolamo • 140
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... Sorry, but what you are asking for are 10 lines of code in python(maximum) and even less in R ...
written 3.0 years ago by
Girolamo • 140
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... like this?
http://rest.kegg.jp/list/compound ...
written 3.0 years ago by
Girolamo • 140
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... Could this DB useful?
http://database.oxfordjournals.org/content/2016/baw035.abstract?sid=4f29cbc1-a695-407c-8b56-60e833889c1e
and the web application:
https://attract.cnic.es/index ...
written 3.0 years ago by
Girolamo • 140
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... I think that the first decimal column refers to the first protein, and so on.
For example: the expression for 4EBP1 is 157.88, the expression of AKT1 is 78.54
What is strange to me is that the 14-3-3, the CTNB1 and PIK3R1 have the same expression.
...
written 3.0 years ago by
Girolamo • 140
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... In my opinion, the decimal numbers in the table represent the expression of the proteins, according to what is written in the caption of the supplementary material: *"Additional file 2: Expression and interaction data related to normal and cancer conditions of five tissues"*
Even if the numbers are ...
written 3.0 years ago by
Girolamo • 140
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