Tag Archives: CRISPR


Friday SNPpets

This week there’s an actual call to action in the tweets. See Steven Salzberg’s tweet about the 2017 Service to America award. You can vote for Genbank. Really–try to imagine the last couple of decades without it. And it’s time to celebrate government science in front of the public. Go vote. After that, come back for the cheese and pomegranite genome. Most intriguing chatter this week was the ancient plant genome stuff at the bottom. I keep trying to tell people how far ahead agriculture is in genomics applications. Human researchers: ZZZZzzzzzzzzz.

SNPpets_2Welcome to our Friday feature link collection: SNPpets. During the week we come across a lot of links and reads that we think are interesting, but don’t make it to a blog post. Here they are for your enjoyment…


Friday SNPpets

This Friday includes a range of topics, as usual. Interesting assessments of the state of autism genomic architecture–and read the piece on the “ghettoization” of genetic disease after that (Laura Hercher’s tweet). Horizontal gene transfer in cheese bacteria. Traits in crops. CRISPR for insects. Deep time in human DNA, and evolutionary history of tumors. There are so many great things around right now…. Off we go!

SNPpets_2Welcome to our Friday feature link collection: SNPpets. During the week we come across a lot of links and reads that we think are interesting, but don’t make it to a blog post. Here they are for your enjoyment…

Friday SNPpets

This week’s SNPpets include the highly topical human migration issues–those that weren’t prohibited by the White House, at least. Speaking of charged issues–the NAS releases the CRISPR-human editing report next week. Also this week–human food crop resources and papers. Quinoa! But one that’s truly key for science is the coffee genome, of course. I’ll bet a disproportionate amount of science world-wide relies on caffeinated grad students. Also: sequencing Filbert. Not the nut. I love crowd-funded genome projects. And I added a nice graphic of clinical mutations that could be useful in public outreach situations. I’m getting more and more interested in doing that.

SNPpets_2Welcome to our Friday feature link collection: SNPpets. During the week we come across a lot of links and reads that we think are interesting, but don’t make it to a blog post. Here they are for your enjoyment…

Friday SNPpets

This week’s SNPpets include The Economist and C&EN cover gene editing in different but useful ways, new software for metagenomics, stranded RNA-Seq, the new CDC Public Health Genomics Knowledge Base, IGB paper, Docker getting attention in biology, FDA precision medicine workshops, a nice popular press version of the ExAc (Exome Aggregate Consortium) story,  and the heresy of Keith Robison who doesn’t hate Excel enough.

Welcome to our Friday feature link collection: SNPpets. During the week we come across a lot of links and reads that we think are interesting, but don’t make it to a blog post. Here they are for your enjoyment…


What’s the Answer? (woolly mammoth ORFs)

This week’s highlighted question was interesting to me in a couple of ways. It was a good question about the recent analysis of the woolly mammoth genome, making it a nice example of post-publication discussion. But mostly I just loved the chatter about issues and challenges around extinct organisms and their sequences. We are living the in the future now. And that’s so awesome.

Biostars is a site for asking, answering and discussing bioinformatics questions and issues. We are members of the Biostars_logo community and find it very useful. Often questions and answers arise at Biostars that are germane to our readers (end users of genomics resources). Every Thursday we will be highlighting one of those items or discussions here in this thread. You can ask questions in this thread, or you can always join in at Biostars.

Question: Where are the mammoth’s ORFs?

Not sure if anyone from the Swedish Museum of Natural History is on this forum but does anyone know any plans to process the bam files from http://www.ebi.ac.uk/ena/data/view/ERP008929 into something we can actually use for looking at protein evolution? Might Ensembl eventualy pick up the data for their pipeline Emily_Ensembl ? and/or the NCBI ? This is not the first time journal editors allow a new genome paper without the genome in question being in any usable form for biologists

“Complete Genomes Reveal Signatures of Demographic and Genetic Declines in the Woolly Mammoth”



I loved Emily’s explanation, and this part: “…mammoths have no active transcription…”. I thought to myself, well, not yet. The Plan to Turn Elephants Into Woolly Mammoths Is Already Underway. George Church and CRISPR are on the way back to the future already.

Video Tip of the Week: CRISPRdirect for editing tools and off-target information

Great RCSB PDB molecule-of-the-month page on CRISPR

Great RCSB PDB molecule-of-the-month page on CRISPR

Genome editing strategies are certainly a hot topic of late. We were astonished at the traffic that the animation of the CRISPR/Cas-9 process recently drew to the blog. There’s a huge amount of potential for novel types of studies and interventions in human disease situations–but I’m already seeing applications in agriculture coming along. There’s an edited canola available in Canada already. China has edited wheat for disease resistance. There’s a project underway to remove horns from cattle–by merely snipping out a bit of sequence with TALENs/ZNF strategies. They’ve already created cattle with edited myostatin too.

To accompany this work, new software tools have been developed to help design target sequences and evaluate potential off-target situations. Both TALEN target software tools exist, and CRISPR tools exist. For this post I’ll be focusing on just one of the CRISPR tools, but I’ll list a few others as well. Some sites have incorporated both options in their software tools. Some will have a small range of species, some have larger sets. So part of choosing a tool is asking about the genomes it supports. In future Tips we may explore some of the others. There is something of a flood of these tools coming along, and I’ll continue to explore them.

This week’s focus is CRISPRdirect. A Japanese group has created this tool for generating a guide sequence and for evaluating potential off-target activity. This introductory video (with music, and with English annotations to convey the features) will give you an overview of the functions.

It seems to be an easy-to-use interface, with effective organization of the results. They have a nice range of species to examine–not only some of the mammalian genomes, but fish, chicken, worm, plants, and yeast too. There’s a graphical viewing component and an easy export option as well.

So I’ve come across a few tools in my search, but if you have favorites please feel free to add them below in the comments. I’m going to continue to look into these tools and will be looking to highlight others in the future.

Quick link:

CRISPRdirect: http://crispr.dbcls.jp/

A few links to other tools I’ve been looking at:

E-TALEN: http://www.e-talen.org/E-TALEN/

E-CRISP: http://www.e-crisp.org/E-CRISP/

TAL Effector Nucleotide Targeter 2.0: https://tale-nt.cac.cornell.edu/

Prognos: http://baolab.bme.gatech.edu/Research/BioinformaticTools/prognos.html

ZiFiT Targeter software (TALEN/ZNF/CRISPR support): http://zifit.partners.org/ZiFiT/

COSMID: https://crispr.bme.gatech.edu/

CRISPY (specific for CHO cells): http://staff.biosustain.dtu.dk/laeb/crispy/


Naito Y., K. Hino, H. Bono & K. Ui-Tei (2014). CRISPRdirect: software for designing CRISPR/Cas guide RNA with reduced off-target sites, Bioinformatics, DOI: http://dx.doi.org/10.1093/bioinformatics/btu743

Genome Editing with CRISPR-Cas9, nifty animation

I saw this come across my twitter feed the other day, and as a nice Friday afternoon diversion I posted it to Google+. I was surprised how popular it was. So I thought–hey, I have a blog too. Let’s put it there…. So grab some coffee and watch, a nice gentle way to get your Monday underway.

This animation depicts the CRISPR-Cas9 method for genome editing – a powerful new technology with many applications in biomedical research, including the potential to treat human genetic disease. Feng Zhang, a leader in the development of this technology, is a faculty member at MIT, an investigator at the McGovern Institute for Brain Research, and a core member of the Broad Institute. Further information can be found on Prof. Zhang’s website at http://zlab.mit.edu .

Images and footage courtesy of Sputnik Animation, the Broad Institute of MIT and Harvard, Justin Knight and pond5.

The publications page at the Zhang lab has some nice examples of CRISPR, including that knockin mouse one with cancer modeling applications. I’ve been meaning to get that but don’t have a subscription to Cell, so that was handy.

Platt R., Sidi Chen, Yang Zhou, Michael J. Yim, Lukasz Swiech, Hannah R. Kempton, James E. Dahlman, Oren Parnas, Thomas M. Eisenhaure, Marko Jovanovic & Daniel B. Graham & (2014). CRISPR-Cas9 Knockin Mice for Genome Editing and Cancer Modeling, Cell, 159 (2) 440-455. DOI: http://dx.doi.org/10.1016/j.cell.2014.09.014