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Dear Dr. Sean,
I hope this message finds you well. I am writing to express my admiration for your recent publication in Current Biology titled "High viral abundance and low diversity are associated…
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Hi, all
I used this nice tool to identify CRISPR-Cas systems for my assembled MAGs. However, the result of the output file (CRISPR-Cas_summary.tsv) doesn't have Cas and Cas Types/Subtypes. Why? Whe…
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This is a reboot of #36 (solved in #40), with a few extra frills.
The classification system developed by [Makarova et al](http://dx.doi.org/10.1038/nrmicro3569) can be translated into a [decision t…
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Dear all
I ran CRISPRCasFinder on some contig sequences that I know contains Cas proteins of various subtypes with the options -cas -def G, but am still getting no Cas type information in my [outpu…
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Hi,
Thank you for creating a great platform to examine the CRISPR-Cas transposon systems bioinformatically!
I was able to follow along the tutorial to find CRISPR and Cas proteins in the genome o…
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Hello,
I installed CRISPRCasFinder using conda. I am running the script on draft genomes. The script is running fine with the fasta files containing less than 100 contigs but is detecting no CRISPR…
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We have discovered recently that a particular set of parameters (quite sensible, in our opinion) for CCF fails to produce any CRISPR arrays for all genomes we tried.
Here is the command line we use…
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## Summary
#### 1. どんなもの?(Abstract,Conclusion)
#### 2. 先行研究と比べてどこがすごいの?(先行研究,どんな問題を解決した)
#### 3. 技術や手法の"キモ"はどこにある?(新規点,どう解決した)
#### 4. どうやって有効だと検証した?(実験手法)
#### 5. 議論はあるか?(未解決点,応用例)
#### 6. 次に読む…
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- [ ] curate viral diversity (identify threshold for viruses)
- [ ] phage bacteria community similarities (beta-diversity coupling)
- [ ] phage bacteria co-occurrences (networks)
- [ ] phage-host p…
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I'd like to be able to design CRISPR guide RNAs with Poly. Below is a draft spec for a new CRISPR package:
## Spec
Our guide RNA design package should be lightweight and easily extendable and at…