User: mossmatters

gravatar for mossmatters
mossmatters90
Reputation:
90
Status:
New User
Location:
Chicago Botanic Garden, Glencoe, IL
Website:
http://mossmatters.net/
Twitter:
mossmatters
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Google Scholar Page
Last seen:
2 years, 9 months ago
Joined:
8 years, 5 months ago
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m*********@gmail.com

Posts by mossmatters

<prev • 9 results • page 1 of 1 • next >
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Comment: C: Where can I download exonerate?
... I can report that the download from the github site above did work. On MacOS 10.10.4 this required: ./configure automake --add-missing make make install ...
written 4.3 years ago by mossmatters90 • updated 18 days ago by RamRS25k
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Where can I download exonerate?
... The website I bookmarked for Exonerate seems to be down: http://www.ebi.ac.uk/~guy/exonerate/ Does anyone know where I can find the latest version of the program? This site seems to be a mirror of the original website, but refers the user to the website that no longer exists: http://www.animalge ...
exonerate written 4.3 years ago by mossmatters90 • updated 2.9 years ago by shrirambhosle30
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Hardware Recommendations: 1 Terabyte of RAM?
... We have a good bit of funding available to purchase a high performance computer, and we are wondering if others have experience setting up and running machines with up to 1 TB of RAM. We are interested in using the computer for de novo genome assembly of plants, and expect the genomes to be highly r ...
hardware genome assembly written 4.5 years ago by mossmatters90 • updated 4.4 years ago by h.mon28k
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Comment: C: Processing Blast XML output generated by GNU Parallel with Biopython SearchIO
... I have the basidiomycota sequences from NR in a custom database, and I am BLASTing an entire proteome against them. I have access to four servers, each of which has 12 CPUs. Some testing I did suggested that limiting the number of jobs parallel would execute, while also using some multi-threading fo ...
written 5.6 years ago by mossmatters90
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Processing Blast XML output generated by GNU Parallel with Biopython SearchIO
... I have been using GNU Parallel to search an organism's entire proteome against a sequence database. It works great for BLAST tabular output, but I would like to use the traditional XML output, because of how well the SearchIO module of Biopython works. Specifically, I am interested in filtering the ...
searchio gnu parallel biopython written 5.6 years ago by mossmatters90 • updated 5.6 years ago by Peter5.8k
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Answer: A: Merging Bootstrap Values And Posterior Probabilities
... Here's an interesting post on the topic, with some solutions using the ape package in R: http://treethinkers.blogspot.com/2008/10/labeling-trees-posterior-probability.html In the comments, the developer of Dendropy points out that his Sumtrees script (http://pythonhosted.org/DendroPy/scripts/sumtre ...
written 5.7 years ago by mossmatters90
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Comment: C: Iteratively Concatenate An Arbitrary Number Of Seq Objects Using Biopython
... Yes, I think a join method would be a good addition to Biopython! ...
written 5.8 years ago by mossmatters90
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Comment: C: Iteratively Concatenate An Arbitrary Number Of Seq Objects Using Biopython
... Thanks! I guess I was just wondering if there was an equivalent to .join for Seq objects. If there were, would it be faster than converting from Seq object to str and then back to Seq object, as you've done? ...
written 5.8 years ago by mossmatters90
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Iteratively Concatenate An Arbitrary Number Of Seq Objects Using Biopython
... What is the best way to join multiple Seq objects together into one sequence? The Biopython tutorial suggests using "+" to join the sequence of two sequence objects: seq3 = seq1+seq2 But what if I had a list (of arbitrary length) of Seq objects? If they were strings I could simply: "".join(seq_ ...
seq biopython written 5.8 years ago by mossmatters90 • updated 5.8 years ago by Peter5.8k

Latest awards to mossmatters

Popular Question 3.7 years ago, created a question with more than 1,000 views. For Iteratively Concatenate An Arbitrary Number Of Seq Objects Using Biopython
Popular Question 3.7 years ago, created a question with more than 1,000 views. For Processing Blast XML output generated by GNU Parallel with Biopython SearchIO
Popular Question 3.8 years ago, created a question with more than 1,000 views. For Processing Blast XML output generated by GNU Parallel with Biopython SearchIO
Popular Question 3.8 years ago, created a question with more than 1,000 views. For Iteratively Concatenate An Arbitrary Number Of Seq Objects Using Biopython
Commentator 4.1 years ago, created a comment with at least 3 up-votes. For C: Where can I download exonerate?

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