User: tigeradab

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tigeradab40
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India
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3 years ago
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6 years, 7 months ago
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Posts by tigeradab

<prev • 11 results • page 1 of 2 • next >
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Comment: C: Machine learning based classification techniques
... No this is no class assignment. SMO used by weka is a different algorithm from the solvers used by LibSVM. Hence, their parameters are quite different. But the question is which one is better? And principally what are the differences?  ...
written 3.1 years ago by tigeradab40
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Machine learning based classification techniques
... I'm a novice in machine learning-based classification techniques. Please do help 1) What is the difference between SMO (weka) and the LibSVM algorithms? Which is the best? Because the parameter requirements of the two are very different.  2) Feature reduction (e.g.PCA) and feature selection (e.g. ...
machine learning written 3.1 years ago by tigeradab40 • updated 2.5 years ago by chen1.7k
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How to retrieve single Ka and Ks values from a whole multiple sequence alignment using PAML (codeml)?
... I am able to retrieve ka/ks ratio for a multiple sequence alignment using the model=0 and NSsites=0 in the .ctl file of PAML. But, I also require the individual ka and ks values for the whole alignment. Is it possible to retrieve this from PAML? If yes, then what parameter should I change in the .ct ...
evolutionary constraints alignment substitutions written 3.3 years ago by tigeradab40 • updated 3.2 years ago by Biostar ♦♦ 20
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Effective Number Of Codons (Enc Vs. Gc3 Plot)
... How to plot the ENC vs GC3 plot showing the curve of expected ENC value? I guess the formula(approximate relationship) given in ENC paper by Wright,1990 has an error. Looking at the formula we can see that always the 29/(s2+(1-s2)) comes to be 29 as s2 cancel out in the denominator. Is there any cor ...
codon written 4.8 years ago by tigeradab40 • updated 4.2 years ago by rahulravi7770
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Codon Adaptation Index
... What are the steps to calculate Codon Adaption Index using codonw? How to give reference set of genes to the codonw software? Other than codonw, is there any other software that computes and gives CAI? Also, is there any software that calculates CAI using Carbone's method? ...
codon index written 4.8 years ago by tigeradab40 • updated 11 days ago by anamaria30
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Comment: C: Codon Adaptation Index
... Thanks for the reply. Yes. It might be a good idea if I want to see deviation of a coding sequence between taxa. But, in my case I would want to see the similarities between coding sequences within the same organism/taxon so as to find out genes which have some correlation like they are similarly ex ...
written 5.0 years ago by tigeradab40
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Codon Adaptation Index
... How to choose a reference set of highly expressed genes for calculating Codon Adaptation Index? What if I do not have any experimental evidence related to their expression levels or on the other hand what if I have a newly annotated genome? Is it still possible to compute CAI? ...
codon genes index written 5.0 years ago by tigeradab40 • updated 5.0 years ago by 5heikki7.8k
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Comparison Of Biological Graphs/Networks
... If I want to compare two biological networks/graphs (as in graph theory) what are the best clustering methods and which method is to be chosen for comparison? Can anyone suggest a good review/article for the same? ...
network graph clustering written 5.1 years ago by tigeradab40 • updated 5.1 years ago by Neilfws48k
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(Closed) Numerical Methods - Root Finding
... How to use Newton Raphson Method for finding roots of a polynomial having more than one possible roots? For example, x2-4x-10 ...
written 6.3 years ago by tigeradab40 • updated 6.3 years ago by Michael Dondrup45k
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Does Anybody Have A Code/Pseudocode For Construction Of Grid Around A Protein?
... Does anybody know how to place a grid of some definite spacing around a protein? Does anybody have a code/pseudocode for doing the same? A code/pseudo code will be helpful. ...
protein written 6.5 years ago by tigeradab40 • updated 23 months ago by Biostar ♦♦ 20

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