User: brian.fristensky

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Canada/University of Manitoba
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http://home.cc.umanito...
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Posts by brian.fristensky

<prev • 10 results • page 1 of 1 • next >
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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 4 weeks ago by brian.fristensky80
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Comment: C: know the grep command for fastq file
... SeqKit works with both fastq and fasta files. ...
written 4 weeks ago by brian.fristensky80
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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 5 weeks ago by brian.fristensky80
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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 5 weeks ago by brian.fristensky80
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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 5 weeks ago by brian.fristensky80 • updated 5 weeks ago by RamRS23k
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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 5 weeks ago by brian.fristensky80
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News: BIRCH Release 3.50
... NEW: Introducing blreads: BioLegato GUI that makes it easy to run programs involving sequencing reads including - read trimming, error correction and quality control - genome assembly and quality assessment - transcriptome assembly and quality assesment - generation of differential expression d ...
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Answer: A: Is there some good software to align/compare fasta sequences in my PC
... [The BIRCH system][1] includes lots of popular tools for sequence tasks. In particular, see the [tutorials page][2] on Pairwise Similarity, as well as Multiple Sequence Alignment. You can see BIRCH in action on our [YouTube Channel][3] BIRCH is freely available for Linux and MacOSX. [1]: http ...
written 5 weeks ago by brian.fristensky80
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Answer: A: Minimum Standards For Bioinformatics Command Line Tools
... One minor point: Error messages should identify which program is generating the message. For example, both the shell and the program might generate a message, so it should be clear which one is responsible. To illustrate from an example above: % biotool --mask reads.fq Error: can't load /h ...
written 2.2 years ago by brian.fristensky80
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Tool: BIRCH Bioinformatics System v 3.40
... **NEW:** - New programs for comparative genomics - New tutorials - Improvements to management of local BLAST databases **BIRCH is** - a comprehensive desktop bioinformatics system which comes with many of the commonly-used bioinformatics programs pre-installed - a framework of tools, files, an ...
genome sequence tool blast written 2.3 years ago by brian.fristensky80

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Teacher 5 weeks ago, created an answer with at least 3 up-votes. For A: Extract specific genes from a FASTA file.

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