User: Manu Madhavan

gravatar for Manu Madhavan
Reputation:
10
Status:
New User
Location:
NIT Calicut
Website:
http://people.cse.nitc...
Last seen:
5 months, 2 weeks ago
Joined:
6 months, 1 week ago
Email:
m*************@nitc.ac.in

Research Scholar

Department of CSE

NIT Calicut, Kerala

India

Posts by Manu Madhavan

<prev • 8 results • page 1 of 1 • next >
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Comment: C: RNA secondary structure - Feature extraction
... Thank you for your clarification. This discussions help me to get more insights on my problem. My study is whether there exist any distinctive structural motif pattern in protein coding RNAs and non-coding RNAs, so that we can use this feature for their identification using machine learning. Based o ...
written 5 months ago by Manu Madhavan10
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Comment: C: RNA secondary structure - Feature extraction
... Thanks a lot!! Your support and suggestions are very useful and motivational. > Do you mean beyond what's done in the code I posted earlier? I mean, what is the algorithm for identifying structural fragments ( as in Fig 2.7 in your master thesis)? What I understand is a fragment may contain mo ...
written 5 months ago by Manu Madhavan10
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Comment: C: RNA secondary structure - Feature extraction
... Thank you for the detailed reply. I started reading your Master thesis, and it help me to get more clear understanding of the secondary structure. I am interested to know more details of definition/identification secondary structure motifs, mentioned in second chapter. If I can represent the secon ...
written 5 months ago by Manu Madhavan10
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Comment: C: RNA secondary structure - Feature extraction
... Thank you for your effort. Let me ask some of my basic doubts (I am sorry if it is too childish) 1. Are base pairs corresponds to stem in secondary structure? 2. In the above example, can I say the structure contain 3 multiloops and 2 hair pins? 4. ['Hairpin', (4, 8)] means nucleotides from pos ...
written 5 months ago by Manu Madhavan10
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Comment: C: RNA secondary structure - Feature extraction
... Thank you for your reply and sharing your insights. When I run your code "mdg_dt.py", got the following output. [Output][1] Could you please help me to interpret this output? [1]: https://ibb.co/dh2Wo8 ...
written 5 months ago by Manu Madhavan10
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RNA secondary structure - Feature extraction
... Hi All, For coding-non coding RNA identification (using Machine learning classifier), I would like to add features extracted from RNA secondary structure. I used RNAfold to get the secondary structure from primary sequence (as dot-bracket representation). Now I want to identify loops, stems, bulges, ...
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Comment: C: Multiple Sequence Alignment Python
... I have used k-mer (k-length substring) frequencies, GC content, Molecular weight ...,. I would like to include features from MSA (some variance from profile sequence) to this feature set. ...
written 6 months ago by Manu Madhavan10
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Multiple Sequence Alignment Python
... Hi, Currently I am working on classifying coding/non coding RNAs based on sequence features. I want to try MSA score as a feature for sequence classification. - Please help me to get MSA score (using Clustlw) for a collection of sequences, using Biopython. - How can I a get a profile seque ...

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