User: NPalopoli

gravatar for NPalopoli
NPalopoli290
Reputation:
290
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Trusted
Location:
Argentina/Buenos Aires/Universidad Nacional de Quilmes
Website:
http://about.me/npalopoli
Twitter:
npalopoli
Scholar ID:
Google Scholar Page
Last seen:
2 months, 3 weeks ago
Joined:
9 years, 5 months ago
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n*******@gmail.com

Computational biologist under natural selection.

Posts by NPalopoli

<prev • 17 results • page 1 of 2 • next >
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Get real model numbers from PDB using BioPython
... Hi, The following piece of code uses Biopython to split all models from a valid PDB file into individual files. It takes a PDB-formatted filename and a PDB code as input (arguments -f and -p respectively) and writes each existing model to a different output PDB file (with filename format "PDBcode ...
biopython structure python2 proteins written 12 weeks ago by NPalopoli290 • updated 12 weeks ago by jgreener240
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Answer: A: How can run cd-hit-est with a clstr threshold less than 0.8?
... According to the [cd-hit-est manual][1] you should use one of the following combinations of threshold (`-c`) and word size (`-n`): > -n 10, 11 for thresholds 0.95 ~ 1.0 > -n 8,9 for thresholds 0.90 ~ 0.95 > -n 7 for thresholds 0.88 ~ 0.9 > -n 6 for thresholds 0.85 ~ 0 ...
written 16 months ago by NPalopoli290
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Answer: A: How To Download The Whole Genome Sequence Of Rat? (Rattus Norvegicus)
... A good place to look for information about genome projects is Genome at NCBI, which "Contains sequence and map data from the whole genomes of over 1000 organisms". http://www.ncbi.nlm.nih.gov/genome Use the search box or follow this link to the rat (Rattus norvegicus) entry: http://www.ncbi.nlm.ni ...
written 6.6 years ago by NPalopoli290
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Answer: A: Find The Second Best Maximum Likelihood Tree
... PAUP can perform maximum-likelihood estimations on phylogenetic trees. You can save all output trees to a file using: savetree file=output.phy format=phylip where format=phylip is optional. If you want to save a subset of the trees, add the arguments from and to; for example, from=1 to=1 will s ...
written 6.6 years ago by NPalopoli290
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Comment: C: Full Structure Of Protein Sequence
... I am not entirely sure what you are asking for. If you just need a database of full proteins then the ProteinDataBank is the place to go. If your protein is not deposited there, or just a part of it is, then you will need to find different template PDBs that cover the total length of your protein an ...
written 7.7 years ago by NPalopoli290
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Check Integrity Of Pdb Files
... Which programs could be used to check the integrity of PDB files? And by that I mean recognize the (minimum) standard PDB format, check if there are missing residues (according to numbering in ATOM lines), missing atoms (according to residue identity and apart from hydrogens), non standard amino aci ...
pdb format written 8.0 years ago by NPalopoli290 • updated 8.0 years ago by João Rodrigues2.5k
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Answer: A: Full Structure Of Protein Sequence
... You should notice that it is very common to find PDB files that do not span the whole length of the actual protein. This may be because the experimentalists have focused on just one domain of a multidomain protein, or because they have not been able to solve the positions of some of its atoms (perha ...
written 8.2 years ago by NPalopoli290 • updated 8 months ago by RamRS27k
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Replace Image To Jmol Representation After Click
... Dear all, I am using jmolApplet to display some PDBs in a web page. I would like to know how to load an image instead by default (possibly a static representation of the PDB), then when the user clicks on the image or an accompanying link the image is replaced by a jmol representation of the same PD ...
pdb web written 8.4 years ago by NPalopoli290 • updated 8.4 years ago by Keith Callenberg900
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Generate Image Of Pdb File From Script Or Command Line
... Hi, I would like to get an image of a PDB file from any given script or command line order. What tools do you know that could fulfill this task? Thanks! ...
pdb tool written 8.4 years ago by NPalopoli290 • updated 5.9 years ago by Biostar ♦♦ 20
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Tools Of Choice For Functional Annotation Of Genes And Proteins
... I would like to know which are the tools you would choose for performing the functional annotation of genes and proteins. It would be very helpful if you could specify the capabilities, the pros and cons and your own experience relating any method you may recommend or not. I am particularly looking ...
annotation function written 8.8 years ago by NPalopoli290 • updated 21 months ago by Biostar ♦♦ 20

Latest awards to NPalopoli

Popular Question 3.2 years ago, created a question with more than 1,000 views. For Generate Image Of Pdb File From Script Or Command Line
Epic Question 3.2 years ago, created a question with more than 10,000 views. For How To Run Clustalw Using Commands From An Input File
Great Question 3.8 years ago, created a question with more than 5,000 views. For Calling Python Script From Bash Console While Using Gnu Parallel
Great Question 4.1 years ago, created a question with more than 5,000 views. For Tools Of Choice For Functional Annotation Of Genes And Proteins
Popular Question 4.7 years ago, created a question with more than 1,000 views. For Generate Image Of Pdb File From Script Or Command Line
Voter 4.8 years ago, voted more than 100 times.
Popular Question 5.2 years ago, created a question with more than 1,000 views. For How To Run Clustalw Using Commands From An Input File
Great Question 5.6 years ago, created a question with more than 5,000 views. For How To Run Clustalw Using Commands From An Input File
Supporter 6.3 years ago, voted at least 25 times.
Teacher 8.2 years ago, created an answer with at least 3 up-votes. For A: Full Structure Of Protein Sequence
Good Question 8.8 years ago, asked a question that was upvoted at least 5 times. For Tools Of Choice For Functional Annotation Of Genes And Proteins
Appreciated 8.8 years ago, created a post with more than 5 votes. For Tools Of Choice For Functional Annotation Of Genes And Proteins
Popular Question 8.8 years ago, created a question with more than 1,000 views. For Tools Of Choice For Functional Annotation Of Genes And Proteins
Student 8.8 years ago, asked a question with at least 3 up-votes. For Tools Of Choice For Functional Annotation Of Genes And Proteins
Popular Question 8.8 years ago, created a question with more than 1,000 views. For Calling Python Script From Bash Console While Using Gnu Parallel
Student 8.8 years ago, asked a question with at least 3 up-votes. For Calling Python Script From Bash Console While Using Gnu Parallel
Student 9.5 years ago, asked a question with at least 3 up-votes. For How To Run Clustalw Using Commands From An Input File
Popular Question 9.5 years ago, created a question with more than 1,000 views. For How To Run Clustalw Using Commands From An Input File

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