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User: brian.fristensky

gravatar for brian.fristensky
Reputation:
140
Status:
Trusted
Location:
Canada/University of Manitoba
Website:
http://home.cc.umanito...
Last seen:
1 week, 2 days ago
Joined:
3 years, 9 months ago
Email:
b***************@umanitoba.ca

I'm an Associate Professor in the Department of Plant Science at the University of Manitoba.

 

Posts by brian.fristensky

<prev • 28 results • page 1 of 3 • next >
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Comment: C: Blast + Alignement Shell Script
... You are right, sometimes you want a shell script for processing large numbers or queries. What I will say is that the GUI interfaces in BIRCH give you access to almost all functionality of the programs it runs, and also saves a lot of the trial and error associated with running searches using script ...
written 5 weeks ago by brian.fristensky • 140
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Answer: A: Blast + Alignement Shell Script
... Rather than writing a shell script, you might want to try out the extensive features in the [BIRCH][1] system that give you a powerful point and click environment for running BLAST, viewing results, retrieving hits, and piping the hits into multiple alignments. For your purposes, you may be partic ...
written 5 weeks ago by brian.fristensky • 140
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Comment: C: blast extract specific gene linux command
... If I interpret your question correctly, you want to find sequences in some other genomes that are similar to your yeast query genes. Then you want to retrieve sequences matching your queries, extract the coding sequences, presumably translate them, remove redundant sequences, do a multiple alignment ...
written 3 months ago by brian.fristensky • 140
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Answer: A: Redundancy removing in sequences
... If you're using Linux or MacOSX you definitely want to try the [BIRCH][1] system. See the BIRCH [Multiple sequence alignments][2] tutorial which shows how to eliminate redundant sequences using CD-HIT. You can learn more about BIRCH on our YouTube channel at [https://www.youtube.com/channel/UC9_ ...
written 3 months ago by brian.fristensky • 140
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Answer: A: file and directory management best practices
... At the risk of sounding stodgy, I'd say that there is no substitute for deliberate and thoughtful organization right from the beginning. Search tools sometimes work, but are often more trouble than they're worth. An example would be most university web sites. If you try to do keyword seaches, you ge ...
written 6 months ago by brian.fristensky • 140
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Comment: C: Resources to learn genome assembly workflow for small genomes (like viruses)
... All Open source, and local. There are a few exceptions to the "local" part, in that you can run a BLAST+ search either using locally-installed copies of NCBI databases, or send the search to be run at NCBI. In either case, output pops up on your screen. As further enticement, BIRCH now sends email ...
written 6 months ago by brian.fristensky • 140
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Comment: C: Resources to learn genome assembly workflow for small genomes (like viruses)
... While there's no denying the power of the command line, [the BIRCH system][1] gives you the best of both worlds: An intuitive object-oriented set of GUI applications that run hundreds of common bioinformatics programs, which can also be run at the command line when that is more convenient. Assembli ...
written 6 months ago by brian.fristensky • 140
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Answer: A: Which tools do you miss?
... As a software developer, you might be intrigued by [Biolegato][1], a programmable GUI that makes it easy for biologists to run command-line programs. BioLegato is a Java application that lets the user set parameters in menus that are specified using PCD, a simple language that my lab has developed s ...
written 6 months ago by brian.fristensky • 140
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News: Software: BIRCH Bioinformatics System 3.70
... BIRCH 3.70 is now available for download at [http://home.cc.umanitoba.ca/~psgendb/local/public_html/BIRCH3.70announcement.html][1] NEW: - improvements and updates for multiple alignment and phylogeny - personalized user settings for BIRCH environment, including NCBI Entrez API keys - NCBI En ...
assembly genome news alignment rna-seq sequence written 7 months ago by brian.fristensky • 140
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Answer: A: How to extract certain CDS from a GenBank file in linux terminal
... See the BIRCH tutorial CREATING DATASETS OF RELATED SEQUENCES at [http://home.cc.umanitoba.ca/~psgendb/birchhomedir/BIRCHDEV/public_html/tutorials/bioLegato/dataset/dataset.html][1] [1]: http://home.cc.umanitoba.ca/~psgendb/birchhomedir/BIRCHDEV/public_html/tutorials/bioLegato/dataset/dataset.h ...
written 7 months ago by brian.fristensky • 140

Latest awards to brian.fristensky

Scholar 6 months ago, created an answer that has been accepted. For A: file and directory management best practices
Autobiographer 6 months ago, has more than 80 characters in the information field of the user's profile.
Teacher 19 months ago, created an answer with at least 3 up-votes. For A: Extract specific genes from a FASTA file.
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