User: ThulasiS

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ThulasiS40
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Posts by ThulasiS

<prev • 33 results • page 1 of 4 • next >
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Answer: A: Is it possible to do enrichment analysis for selected genes just with GO number
... I found my answer finally We can do it in blast2go. First map the whole protein database which act as universe and retrieve annotation file from your results in blast2go and then upload your test ids list and run gene enrichment analysis. Thats all. ...
written 12 days ago by ThulasiS40
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Comment: C: Is it possible to do enrichment analysis for selected genes just with GO number
... I am using blast2go to get GO numbers. When I am doing Fisher's exact test it was saying no result. Then I read about topGO and GOstats packages from R. So, I asked here. Now, I understood we need two gene sets for enrichment analysis. One acts as universe. Thank you ...
written 13 days ago by ThulasiS40
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Is it possible to do enrichment analysis for selected genes just with GO number in topGO?
... I would like to get Fisher's exact Test, FDR value for certain selected genes. But later i understood that can be done only if we have expression data along with GO number. But in one article they did without any expression data. I am confused, really is it possible to carry gene enrichment analysis ...
R enrichment analysis written 13 days ago by ThulasiS40
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Answer: A: Regarding Whole Genome Visualization
... I suggest you to use MAUVE for visualization of your contigs and part from that have a look at CCT-view for whole genome visualization. Refer: J.R. Grant, A.S. Arantes, P. Stothard, “Comparing thousands of circular genomes using the CGView Comparison Tool” BMC Genomics 13, 202, 2012. It may help yo ...
written 3 months ago by ThulasiS40
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How to analyze multiple codeml output files to find out positive gene clusters?
... Hi all, After long struggle with codeml, finally I was able get the codeml results for my orthologues of interest. Now the major problem ahead of me is to analyze the codeml output and get the positively selected genes list. How can I achieve that, I am not getting any idea. I found some python scr ...
perl python codeml written 3 months ago by ThulasiS40
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What would be the best model to calcualte dn/ds ratio of genes of bacterial strains?
... I am trying to calculate dn/ds ratio for positively selected gene clusters. I am confused with the different models to implement in codeml. Could you suggest best model in codeml for this analysis? ...
dn/ds paml codeml kaks written 3 months ago by ThulasiS40
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Comment: C: Problem with Shell script to automate codeml
... Oh.. yes.. I didn't notice that but even after modifying script also the calculation was going but ended with this error again `Time used: 0:11 Saureus1203.aln Saureus1203.aln Saure_omega.out Traceback (most recent call last): File "codemlScript.py", line 45, in results = cml.run(verbose=Tru ...
written 3 months ago by ThulasiS40
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Comment: C: Problem with Shell script to automate codeml
... Hi Pierrie, now I modified question and description, I missed that '_' in script but still error is there. Sorry for disturbing you. Please check my query. Thank you ...
written 3 months ago by ThulasiS40
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Comment: C: Problem with Shell script to automate codeml
... Output of ls *.phy. aln is Saureus1202.phy.aln Saurues1203.phy.aln ...
written 3 months ago by ThulasiS40 • updated 3 months ago by Pierre Lindenbaum103k
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Comment: C: Problem with Shell script to automate codeml
... This was the error I got after your modification Saureus1202.phy.aln_.aln Saureus1202.phy.aln_.aln Saure_omega.out Traceback (most recent call last): File "codemlScript.py", line 45, in results = cml.run(verbose=True) File "/usr/local/lib/python2.7/dist-packages/Bio/Phylo/PAML/codeml.py", ...
written 3 months ago by ThulasiS40

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