User: ishengomae

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ishengomae100
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Location:
Tanzania, United Republic Of
Last seen:
11 months, 3 weeks ago
Joined:
5 years, 2 months ago
Email:
i*********@nm-aist.ac.tz

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Posts by ishengomae

<prev • 38 results • page 1 of 4 • next >
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Comment: C: Species tree vs Gene trees during evolutionary analyses: Does it matter?
... I was able to follow a main suggestion, that is apply a gene tree for my analysis and it turned out that most of my gene trees were concordant with species phylogeny. And there were no problem anyway in publishing the results e.g. https://www.nature.com/articles/ncomms11519. ...
written 12 months ago by ishengomae100
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Comment: C: How to statistically test significance of molecular convergence in two unrelated
... This looks like what I want. Thanks. ...
written 2.3 years ago by ishengomae100
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How to statistically test significance of molecular convergence in two unrelated lineages
... Hi Biostars, This question is exactly what I need, https://www.biostars.org/p/109405/, but surprisingly, it hasn't received any response for over two years. I'm at a point where I want to test whether convergent changes between the two unrelated lineages are random or not. This paper kind of esta ...
R molecular convergence statistics written 2.3 years ago by ishengomae100 • updated 2.3 years ago by ddiez1.7k
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Identifying interactors of hub genes using Cytoscape Network Analyzer plugin
... I have used Network-Analyzer Cytoscape plugin to identify hub proteins - nodes with the highest node degree distribution - in my protein-protein interaction networks. Now I would like to identify nodes interacting with my hub proteins. I want to perform an enrichment analysis (with cytoscape plugin ...
networkanalyzer cytoscape biological process written 2.9 years ago by ishengomae100 • updated 16 months ago by Biostar ♦♦ 20
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Classifying proteins as enzymes, GPCRs, ion channels, etc.
... I want to produce a simple classification of my proteins in my list based on whether they are enzymes, GPCRs, transducers, neurotransmitters, transcription factors, etc. Is there a way to automatically generate that sort of classification? (I'm imagining of a open source tool that would take gene s ...
gene protein rna-seq written 3.0 years ago by ishengomae100 • updated 3.0 years ago by Dan Gaston7.1k
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Coloring nodes using Cytoscape based on gene to pathway annotation information
... Hi, I want to overlay pathway information to genes, mapped onto Biogrid database accessible via Cytoscape and visualize using Cytoscape. Basically I have about 200 overexpressed genes and I have obtained information about which pathways they map. According to various answers here it seems I have ...
pathway gene network cytoscape biogrid written 3.6 years ago by ishengomae100 • updated 3.6 years ago by AndreiR50
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Tools to analyze/relate protein structural information to its 3D information
... Hi all. Please I'm doing certain evolutionary analysis using Ziheng Yang's PAML/codeml and normally the tool will predict certain amino acid residues to be 'positively selected sites'. Now which tool will help me take these positive sites and then visualize their relationships to the three dimensio ...
gene 3d protein active site written 4.3 years ago by ishengomae100 • updated 4.3 years ago by a.polo88100
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Comment: C: Species tree vs Gene trees during evolutionary analyses: Does it matter?
... Thanks for the (very) helpful reply. ...
written 4.5 years ago by ishengomae100
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Comment: C: How to programmatically query NCBI Gene database
... Thanks to all for the help. ...
written 4.6 years ago by ishengomae100
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How to programmatically query NCBI Gene database
... Hi all. Is there a way by which I can programmatically access the NCBI Gene Database? I have a number of gene names (HGNC gene symbols) of which I want to get a summary of gene function and some literature about those genes. I find the NCBI gene database to be a good place to do this: http://www.nc ...
ncbi gene database biopython R written 4.6 years ago by ishengomae100 • updated 2.8 years ago by govardhanks20

Latest awards to ishengomae

Popular Question 2.3 years ago, created a question with more than 1,000 views. For Coloring nodes using Cytoscape based on gene to pathway annotation information
Popular Question 2.3 years ago, created a question with more than 1,000 views. For Identifying interactors of hub genes using Cytoscape Network Analyzer plugin
Popular Question 2.3 years ago, created a question with more than 1,000 views. For How To Remove All Sequences In My Custom Blast Database?
Popular Question 2.3 years ago, created a question with more than 1,000 views. For How to test for convergent/parallel evolution in a group of homologous proteins?
Popular Question 2.3 years ago, created a question with more than 1,000 views. For How to programmatically query NCBI Gene database
Popular Question 2.3 years ago, created a question with more than 1,000 views. For Online blast and standalone blast return different hits?
Popular Question 2.3 years ago, created a question with more than 1,000 views. For GO terms annotation file format to use in PANTHER
Popular Question 2.9 years ago, created a question with more than 1,000 views. For How to programmatically query NCBI Gene database
Popular Question 3.6 years ago, created a question with more than 1,000 views. For How to programmatically query NCBI Gene database

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