User: Manu Madhavan
Manu Madhavan • 10
- Reputation:
- 10
- Status:
- New User
- Location:
- NIT Calicut
- Website:
- http://people.cse.nitc...
- Last seen:
- 3 months, 3 weeks ago
- Joined:
- 4 months, 3 weeks ago
- Email:
- m*************@nitc.ac.in
Research Scholar
Department of CSE
NIT Calicut, Kerala
India
Posts by Manu Madhavan
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... 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 3 months ago by
Manu Madhavan • 10
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... 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 3 months ago by
Manu Madhavan • 10
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... 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 3 months ago by
Manu Madhavan • 10
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... 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 4 months ago by
Manu Madhavan • 10
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... 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 4 months ago by
Manu Madhavan • 10
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... 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, ...
written 4 months ago by
Manu Madhavan • 10
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... 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 4 months ago by
Manu Madhavan • 10
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... 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 ...
written 4 months ago by
Manu Madhavan • 10
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