User: Kartik Sunagar

gravatar for Kartik Sunagar
Reputation:
290
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Trusted
Location:
Porto, Portugal
Scholar ID:
Google Scholar Page
Last seen:
4 years, 3 months ago
Joined:
9 years, 7 months ago
Email:
a**********@gmail.com

Posts by Kartik Sunagar

<prev • 33 results • page 1 of 4 • next >
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Comment: C: BLAST search against the genome
... Hey. Thanks for that quick reply. Exactly why I wonder if I need to assemble these transcripts into a scaffold before BLAST searching against it. ...
written 6.1 years ago by Kartik Sunagar290
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BLAST search against the genome
... Dear all, I apologize for asking a very basic question. Using local BLAST searches against a genome, I am trying to retrieve full length homologous sequences of a gene of interest. Ultimately, I am interested in knowing the copy number of these genes and would also like to retrieve pseudogenes, if ...
blast written 6.1 years ago by Kartik Sunagar290 • updated 6.0 years ago by Biostar ♦♦ 20
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Answer: A: How Can I Use Paml To Calculate The Dn/Ds Value Of Only Some Specific Branches?
... I suggest trying the Branch-site REL implemented on datamonkey instead. I strongly recommend not using the free-ratio model since it is very parameter rich and is discouraged by the author of the software itself. ...
written 7.7 years ago by Kartik Sunagar290
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Answer: A: Recombination Breakpoint Detection
... I suggest trying SBP algorithm implemented in Datamonkey. Its fast and straightforward. There is another algorithm called GARD on the same server, but SBP supersedes GARD. You could also try RDP4 or RAT All the best! ...
written 7.7 years ago by Kartik Sunagar290
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Comment: C: Color Pdb According To Amino-Acid Conservation
... Thanks man, I'll try that :) ...
written 9.3 years ago by Kartik Sunagar290
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Comment: C: Color Pdb According To Amino-Acid Conservation
... Thank you very much for the reply Michael and Dan. Cheers, Kartik ...
written 9.3 years ago by Kartik Sunagar290
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Comment: C: Color Pdb According To Amino-Acid Conservation
... Hey, that will be awesome! Please do send it if you are allowed (anaturalist@gmail.com). Consurf is a handy tool and I have used it but for some reason I don't find it satisfying. Many times I have noticed that even highly conserved regions are depicted as varying. The author says it could be becaus ...
written 9.3 years ago by Kartik Sunagar290
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Comment: C: Color Pdb According To Amino-Acid Conservation
... Awesome! Thanks a lot.. I've been using Pymol mostly cause I love the interface and images it generates. I hope I find out something similar in pymol too. ...
written 9.3 years ago by Kartik Sunagar290
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Color Pdb According To Amino-Acid Conservation
... Hi, Can you guys suggest to me any tool that can color the pdb file based on the amino-acid conservation using the MSA? I am aware of websites like Consurf that calculate the evolutionary conservation of amino-acids. But I am looking for a simple tool that could highlight only those regions that ar ...
amino-acids conservation pdb written 9.3 years ago by Kartik Sunagar290 • updated 6.3 years ago by Jose Manuel Duarte300
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Answer: A: Protein Sequence Alignment Based On 3D Structure Alignment- For Windows
... Promals3D is one of the best imo.. ...
written 9.3 years ago by Kartik Sunagar290

Latest awards to Kartik Sunagar

Great Question 5.2 years ago, created a question with more than 5,000 views. For Color Pdb According To Amino-Acid Conservation
Popular Question 5.2 years ago, created a question with more than 1,000 views. For Setting Up A Mpi Environment
Popular Question 5.2 years ago, created a question with more than 1,000 views. For Beast - Divergence Time Estimation For Recombinant / Positively Selected Genes
Good Question 6.4 years ago, asked a question that was upvoted at least 5 times. For Color Pdb According To Amino-Acid Conservation
Autobiographer 7.1 years ago, has more than 80 characters in the information field of the user's profile.
Appreciated 9.3 years ago, created a post with more than 5 votes. For Color Pdb According To Amino-Acid Conservation
Student 9.3 years ago, asked a question with at least 3 up-votes. For Color Pdb According To Amino-Acid Conservation
Student 9.5 years ago, asked a question with at least 3 up-votes. For Functional Divergence
Student 9.5 years ago, asked a question with at least 3 up-votes. For Setting Up A Mpi Environment
Popular Question 9.5 years ago, created a question with more than 1,000 views. For Setting Up A Mpi Environment
Popular Question 9.6 years ago, created a question with more than 1,000 views. For Paml - Branch-Site Models
Teacher 9.6 years ago, created an answer with at least 3 up-votes. For A: Multiple Sequence Alignment Of Thousands Of Proteins

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