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User: brian.fristensky

gravatar for brian.fristensky
Reputation:
90
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Location:
Canada/University of Manitoba
Website:
http://home.cc.umanito...
Last seen:
1 day, 1 hour ago
Joined:
3 years, 1 month ago
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b***************@umanitoba.ca

Posts by brian.fristensky

<prev • 14 results • page 1 of 2 • next >
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Answer: A: Intall local BLAST in Ubuntu
... This video goes through the considerations regarding BLAST searches in Linux, as well as graphical tools for installing, managing and searching your local BLAST databases. VIDEO: [Installing BLAST Databases on Your Own Computer][1] [1]: https://www.biostars.org/p/442550/ ...
written 25 days ago by brian.fristensky • 90
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Answer: A: How to filter BLAST results by query coverage? How to analyze large BLAST output
... Have a look at the BIRCH system, which gives you graphical interfaces for running BLAST searches, and for working with the output in spreadsheet form. The Biolegato spreadsheet lets you quickly go through hundreds of hits, and directly retrieve the sequences you choose into sequence sequence tools f ...
written 25 days ago by brian.fristensky • 90
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Tutorial: VIDEO: Installing BLAST Databases on Your Own Computer
... The BIRCH/BioLegato system provides easy point-and-click tools for installing, updating and searching BLAST databases on your own computer. This video describes some of the things you need to consider if you plan to install local copies of BLAST databases, including disk space and network download l ...
linux tutorial sequence blast databases macosx written 25 days ago by brian.fristensky • 90
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Tutorial: VIDEO: BLAST Searches Through a Data Science Lens
... There's a lot more to BLAST searches than just running BLAST. Using the Covid19 spike protein as an example, we'll show how the BIRCH/BioLegato system implements Data Science principles to do database searches that are more informative, and to pipe your results directly into downstream analysis. Sea ...
data science covid19 sequence tutorial blast written 25 days ago by brian.fristensky • 90
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Comment: C: Extract specific genes from a FASTA file.
... I agree, the site uses pretty basic HTML. In fact, if I had it in the budget, I would probably do exactly that. The ToDo list is very long, and like a lot of things in bioinformatics, new features and bug fixes tend to get priority. ...
written 11 months ago by brian.fristensky • 90
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Comment: C: know the grep command for fastq file
... SeqKit works with both fastq and fasta files. ...
written 11 months ago by brian.fristensky • 90
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Comment: A: know the grep command for fastq file
... See answer at [https://www.biostars.org/p/390692/][1] [1]: https://www.biostars.org/p/390692/ ...
written 11 months ago by brian.fristensky • 90
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Answer: A: Best Genome Assembler and Genome Annotation tools and pipelines
... For de-novo genome assembly, you may wish to try the BIRCH system, which runs many of the popular assembly steps including read quality checking, trimming, error correction, and de-novo assembly using SOAPdenovo2, Spades or ABySS, and generates reports on assembly quality using Quast. All of these s ...
written 11 months ago by brian.fristensky • 90
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Answer: A: Extract specific genes from a FASTA file.
... A more general solution is to use by Wei Shen. [SeqKit][1] is a program that does quite a large number of convenient things with fasta/fastq files, and is efficient for big files. Example: If I have a fasta file containing chitinase sequences and I want to extract sequences whose names contain th ...
written 11 months ago by brian.fristensky • 90 • updated 11 months ago by RamRS ♦ 27k
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Answer: A: error when running blastn
... You may wish to try [BIRCH][1], a comprehensive bioinformatics package, which includes desktop tools for installing and managing local copies of BLAST, and doing BLAST searches, automated through our BioLegato applications. BLAST is demonstrated in a recent video: BIRCH - [Desktop Bioinformatics ( ...
written 11 months ago by brian.fristensky • 90

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Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Extract specific genes from a FASTA file.
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