User: natasha.sernova
natasha.sernova • 3.0k
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Posts by natasha.sernova
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... I’ve just asked a fragment of your question in google.
‘comparing two time series gene expression studies’
It gave a lot of omics-tools and other links, for example:
Time-course data analysis software tools
https://omictools.com/time-course-category
A PNAS paper that looks interesting.
http:// ...
written 9 days ago by
natasha.sernova • 3.0k
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... This a general review, it may clear some points.
Divergence and Convergence in Enzyme Evolution
Michael Y. Galperin and Eugene V. Koonin
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3249071/ ...
written 10 days ago by
natasha.sernova • 3.0k
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... There is a classical example - a sea star and a sea urchin
https://www.sciencedirect.com/science/article/pii/S0012160607013425
Caught in the evolutionary act: Precise cis-regulatory basis of difference
in the organization of gene networks of sea stars and sea urchins
As far as I remember, the ar ...
written 12 days ago by
natasha.sernova • 3.0k
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... I am not sure you need any whole genome alignment tool for that.
The ID you need is 16S rRNA, it is called a 'bacterial signature'
See this article from 2012.
Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that
represent uncultured species
http://www.microbi ...
written 15 days ago by
natasha.sernova • 3.0k
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Comment:
C: Get Gene Expression from Gene ID
... I.ve found a link from EBI that helps to do it manually.
You can find the information you've ask about by yourself.
Click a link LATEST in the upper left corner of Biostars.org - page.
Type
protein expression
to the empty line below the menu (instead of 'Live search: start typing ...').
Yo ...
written 19 days ago by
natasha.sernova • 3.0k
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... There is a gene expression Atlas.
https://www.ebi.ac.uk/gxa/home
And it does accept Uniprot id.
You have to give it some additional information.
Gene / Gene properties (Enter gene query…)
Examples: REG1B, zinc finger, O14777 (UniProt), GO:0010468 (regulation of gene expression)
Organism
Bio ...
written 21 days ago by
natasha.sernova • 3.0k
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... It's a mixture of constant arguments and changing arguments.
ad3 ad4 var3 ad5 ad6
Fortunately var3 can be considered constant as well.
But in general case the solution looks more complicated. ...
written 22 days ago by
natasha.sernova • 3.0k
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... Thank you very much, I didn't know so many different ways exist. ...
written 22 days ago by
natasha.sernova • 3.0k
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... Dear all,
My colleague wrote a Python2-script (there is no needed updated library in Python3 ).
To run it, I type
python script.py var1 var 2 ad1 ad2 ad3 ad4 var3 ad 5 ad6 ad7 ad8 ad9 –o var1_ouput.txt
var1, var2, var3 – are changed every run
ad1 ad2 ad3 ad4 ad 5 ad6 ad7 ad8 ad9 – are the ...
written 24 days ago by
natasha.sernova • 3.0k
• updated
23 days ago by
finswimmer ♦ 3.6k
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Comment:
C: Protein binding domain database
... See this article.
iPfam: a database of protein family and domain interactions found in the Protein Data Bank
https://academic.oup.com/nar/article/42/D1/D364/1061536
iPfam looks helpful. ...
written 25 days ago by
natasha.sernova • 3.0k
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