User: natasha.sernova

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natasha.sernova3.0k
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Posts by natasha.sernova

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Comment: C: Comparing time series expression data
... 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.sernova3.0k
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Comment: C: How to characterise a protein "enzyme", and find evolutionary divergence into tw
... 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.sernova3.0k
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Comment: C: more transcriptional factors involved lead to quick or slow phenotype transition
... 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.sernova3.0k
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Answer: C: Software to find Molecular IDs
... 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.sernova3.0k
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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.sernova3.0k
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Answer: C: Get Gene Expression from Gene ID
... 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.sernova3.0k
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Comment: C: How to run Py-script 300 times with 3 new variables and a new output-file each t
... 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.sernova3.0k
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Comment: C: How to run Py-script 300 times with 3 new variables and a new output-file each t
... Thank you very much, I didn't know so many different ways exist. ...
written 22 days ago by natasha.sernova3.0k
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How to run Py-script 300 times with 3 new variables and a new output-file each time?
... 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 ...
python 2 output written 24 days ago by natasha.sernova3.0k • updated 23 days ago by finswimmer3.6k
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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.sernova3.0k

Latest awards to natasha.sernova

Popular Question 5 weeks ago, created a question with more than 1,000 views. For Tools to find the unique proteins (without orthologs) in a bacterial taxon
Popular Question 10 weeks ago, created a question with more than 1,000 views. For Tools to find the unique proteins (without orthologs) in a bacterial taxon
Popular Question 3 months ago, created a question with more than 1,000 views. For Tools to find the unique proteins (without orthologs) in a bacterial taxon
Popular Question 3 months ago, created a question with more than 1,000 views. For Tools to find the unique proteins (without orthologs) in a bacterial taxon
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: dN/dS ratio (omega)
Popular Question 10 months ago, created a question with more than 1,000 views. For Tools to find the unique proteins (without orthologs) in a bacterial taxon
Popular Question 12 months ago, created a question with more than 1,000 views. For Tools to find the unique proteins (without orthologs) in a bacterial taxon
Scholar 12 months ago, created an answer that has been accepted. For A: dN/dS ratio (omega)
Epic Question 15 months ago, created a question with more than 10,000 views. For how to convert a long fasta-file into many separate single fasta sequences
Teacher 16 months ago, created an answer with at least 3 up-votes. For A: dN/dS ratio (omega)
Scholar 18 months ago, created an answer that has been accepted. For A: dN/dS ratio (omega)
Popular Question 19 months ago, created a question with more than 1,000 views. For Tools to find the unique proteins (without orthologs) in a bacterial taxon
Popular Question 19 months ago, created a question with more than 1,000 views. For Tools to find the unique proteins (without orthologs) in a bacterial taxon
Popular Question 19 months ago, created a question with more than 1,000 views. For vcf to MAF to fasta
Scholar 19 months ago, created an answer that has been accepted. For A: dN/dS ratio (omega)
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Commentator 20 months ago, created a comment with at least 3 up-votes. For C: How to find a conserved regions for a protein by phylogentic analysis tree
Student 21 months ago, asked a question with at least 3 up-votes. For how to convert a long fasta-file into many separate single fasta sequences
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Scholar 23 months ago, created an answer that has been accepted. For A: dN/dS ratio (omega)
Scholar 23 months ago, created an answer that has been accepted. For A: dN/dS ratio (omega)

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