User: Zach Powers

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Zach Powers340
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Posts by Zach Powers

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Comment: C: Compare Two Molecular Structures And Generate An Image Highlighting The Differen
... Thank You Sukhi. I was not clear enough in my original post, however, as I am interested in looking at small molecule compounds and essentially performing a substructure search. ...
written 8.4 years ago by Zach Powers340
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Compare Two Molecular Structures And Generate An Image Highlighting The Differences
... I am interested in comparing the molecular structure of a known small molecule compound, say Naphthalene, against a small library of similar compounds. I would like to perform a substructure search of my molecule against the library and then programatically display the results in a way that highligh ...
chemoinformatics written 8.4 years ago by Zach Powers340 • updated 8.4 years ago by Priyanka30
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Answer: A: Identifying Phylogeny Visualisation Software
... check out the ETE2 library for python. There are options for many types of flashy customizations to a phylogenetic tree. zach cp ...
written 8.4 years ago by Zach Powers340
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Answer: A: R: How To Access The Content Of A Cell
... there are lots of ways to manipulate strings in R. Check out this stackoverflow post as a good place to start - the answers include use of gsub, and the stringr package, both of which might be useful for you. good luck! zach cp ...
written 8.4 years ago by Zach Powers340
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Answer: A: Problems Installing Biopython On Mac
... I would recommend installing via MacPorts. Once installed you can simply do: sudo port install py27-biopython #for python2.7 or below for python 2.6 sudo port install py26-biopython these will get all dependencies and will avoid any potential 32bit 64bit problems you may encounter with compiling ...
written 8.5 years ago by Zach Powers340
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Comment: C: Galaxy Taxonomy Output To Newick Tree
... jhc, the tree varies depending on the experiment but a few thousand is typical. I actually came across your Taxonomy Lookup and have been playing with it. It is similar to Pierre's but outputs the newick tree which I can then use with the ETE2 library for custom layout. (which is awesome - thanks!) ...
written 8.5 years ago by Zach Powers340
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Comment: C: Galaxy Taxonomy Output To Newick Tree
... Pierre, thank you. This is basically what I am looking for except that I am unfamiliar with the gexf format. Is it possible to control tree shape/appearance? -- (I don't see anything like a phylogenetic tree in the Gephi documentation.) ...
written 8.5 years ago by Zach Powers340
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Galaxy Taxonomy Output To Newick Tree
... Hi Biostars, I would like to take the output of Galaxy's Metagenomic Analyses > Fetch Taxonomic representation and make a Taxonomic tree that contains abundance information. For display, I could then experiment with the the many excellent visualization softwares out there ( i am particualry in ...
galaxy taxonomy written 8.5 years ago by Zach Powers340 • updated 8.5 years ago by Pierre Lindenbaum131k
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Comment: C: Visualize / Highlight Specific Nodes In A Taxonomy Tree
... jhc,great idea. I would like to do something similar only start with the Tree-of-Life and assign abunce values. However I can't seem to open the NCBI Taxonomy trees (http://itol.embl.de/other_trees.shtml) with ETE2. I would love to copy your general method but using the entire taxonomical dataset ...
written 8.5 years ago by Zach Powers340
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Comment: C: Strategizing Blast Result Parsing
... the more general result I want is to obtain is all unique sequences in NCBI-NT that are related to my start set. I was planning on iteratively BLASTING until I stop turning up new sequences and therefore wanted to keep track of HSPs so I can keep track each round. In order to do this I was keeping t ...
written 8.6 years ago by Zach Powers340

Latest awards to Zach Powers

Appreciated 7.1 years ago, created a post with more than 5 votes. For A: Identifying Phylogeny Visualisation Software
Popular Question 7.1 years ago, created a question with more than 1,000 views. For Galaxy Taxonomy Output To Newick Tree
Popular Question 7.1 years ago, created a question with more than 1,000 views. For User Manual For Genomediagram
Popular Question 7.1 years ago, created a question with more than 1,000 views. For Biopython Parsing Of Blast Results - String Format Issue
Popular Question 7.1 years ago, created a question with more than 1,000 views. For Make A Custom Blast Library Using The Output Of Another Blast Result
Popular Question 7.1 years ago, created a question with more than 1,000 views. For Strategizing Blast Result Parsing
Popular Question 7.1 years ago, created a question with more than 1,000 views. For Biopython Primer Design
Popular Question 7.1 years ago, created a question with more than 1,000 views. For Gff Biopython Parse Issue
Popular Question 7.1 years ago, created a question with more than 1,000 views. For Parse Ncbixml Output Into A Python List Of Hits
Popular Question 7.1 years ago, created a question with more than 1,000 views. For Custom Blast Db On Galaxy Server
Popular Question 7.1 years ago, created a question with more than 1,000 views. For Setup Galaxy Server As A Non-Root System Service
Popular Question 7.1 years ago, created a question with more than 1,000 views. For Compare Two Molecular Structures And Generate An Image Highlighting The Differences
Voter 7.1 years ago, voted more than 100 times.
Supporter 7.1 years ago, voted at least 25 times.
Teacher 7.1 years ago, created an answer with at least 3 up-votes. For A: Problems Installing Biopython On Mac
Teacher 7.1 years ago, created an answer with at least 3 up-votes. For A: Identifying Phylogeny Visualisation Software
Student 7.1 years ago, asked a question with at least 3 up-votes. For Make A Custom Blast Library Using The Output Of Another Blast Result
Student 7.1 years ago, asked a question with at least 3 up-votes. For Custom Blast Db On Galaxy Server
Student 7.1 years ago, asked a question with at least 3 up-votes. For Setup Galaxy Server As A Non-Root System Service

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