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Kevin McKernan 🙂 Profile picture
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Feb 7 • 7 tweets • 4 min read
Psilocybe cubensis assembly in NCBI.
This couldn't be done without @PhaseGenomics or @PacBio

ncbi.nlm.nih.gov/Traces/wgs/JAF…
These HiC maps were performed on spores which express no controversial compounds.
Illumina libraries are also generated with spore preps.
This is the HiC map that organized the 32 contigs of the 1st genome release into 13 chromosomes, Mito and a few small contigs.
The HiFi data provides nice resolution over the Telomeres. These are some genes tucked right up next to these so getting them properly organized is important.
The HiFi data also helps to resolve repeat structures that are longer than the Illumina reads.
There are 81 more genomes that we put public in NCBI that were derived from Illumina sequencing spore preps.
f1000research.com/articles/10-961

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More from @Kevin_McKernan

Kevin McKernan 🙂 Profile picture
Jan 26
Carl Fuller et al are at it again.

This is wild. 16,384 CMOS chip capable of single molecule movies at each pixel.

Each pixel has a protein nanowire bridging it. These are assembled with electrophoresis.

Once wired, click chemistry binds one molecule.

pnas.org/content/pnas/1…
20nM gap for the nanowire peptide bridge.

1000Hz read outs. 0-400pAmp sensors.
Chip features
Read 5 tweets
Kevin McKernan 🙂 Profile picture
Jan 22
Many people ask me about this Moderna patent sequence.

Some calc the odds of a 19mer by chance as 4^19.
A big number if life were truly random.
But evolution is a preservation of those random words that improve fitness so we have to ask, are there similarities to common words?
Take the 19mer sequence and plug it into NCBI BLASTn against the Nr database.

Check ‘exclude’ and enter coronaviridae.

You’ll get microbial hits like this.

Check the E-Value.
What’s the E-Value?
Q: What is the Expect (E) value?
The Expect value (E) is a parameter that describes the number of hits one can “expect” to see by chance when searching a database of a particular size. It decreases exponentially as the Score (S) of the match increases.
Read 8 tweets
Kevin McKernan 🙂 Profile picture
Jan 17
If you read the Corman Drosten retraction demand addendum, you will see we voice concerns over both FN and FPs.

A common newb retort is that the test can’t have both.
On an individual test this is true but on a population level this is false.

pubmed.ncbi.nlm.nih.gov/34741305/
So why do we only hear debate about the FP rate?

I believe this is because the implications of FPs are less severe than the implications of FNs.

FPs you can confirm with another test or just suck it up and quarantine for the ‘greater good’.
FNs, on the other hand, expose the entire track trace system as the scam that it is.

Particularly when they are this high.
Once negative, very few people want to stand in a line with other potentially sick people and pay $50-300 a second shot at quarantine.
Read 4 tweets
Kevin McKernan 🙂 Profile picture
Jan 15
We have Cannabis Whole Genome Sequencing honed to the point where people are using it to untangle the history of the famous Skunk #1 line.

I wasnt around then so I cant speak with any authority on the oral history but I can help people better understand Kannapedia.net
Phylo-Trees can be complicated so lets just take a look at the genetics of THCAS.
There are a few interesting mutations found in early cannabis lines that we will go over.
Ala250Asp
Pro333Arg
Pro542Leu
Ser355Asn
A recently sequenced Skunk line
kannapedia.net/strains/rsp124…
A250D and Pro333Arg are some of the most common mutations.
A250D is found in 12.7% of the NGS data. The C90 data finds this more frequently but less samples have been run through that pipeline.
P333R is found in 18.2% of the NGS data.

Click on the blue %Number
Read 16 tweets
Kevin McKernan 🙂 Profile picture
Jan 8
Respiratory viruses have been around longer than any Judge. To assume parasitism and not mutualism is myopic.
45% of our genome consist of viral elements (LINE, Alu etc) and 8% of the genome consists of infectious retroviruses.

ncbi.nlm.nih.gov/labs/pmc/artic…

annualreviews.org/doi/abs/10.114…
Zero virus plans assume viruses that may be pathogenic for some age groups can be mutualistic for others.

ncbi.nlm.nih.gov/labs/pmc/artic…
The advent of NextGen sequencing allowed us to peer into mutualistic viruses, as in the past, expensive sequencing was reserved for exploring pathogens.

pnas.org/content/118/10…
Read 5 tweets
Kevin McKernan 🙂 Profile picture
Jan 5
An octogenarian in diapers is centrally planning 330M people’s health care with disastrous results…

Many citizens like it

Cheer it on

Even argue for more

Not because it is rational but because they need their tribe to form their identity.

Insecurity induced Munchausen’s.
Much talk about Ass Formation.

I prefer the moniker “Munchausen’s by internet”

ncbi.nlm.nih.gov/pmc/articles/P…
This is an interesting read on how Facebook performed a psychological experiment on 860K of its customers without an IRB.

What’s not to like about spreading massive-scale emotional contagion?

Can I get a side of spike protein with that?

pnas.org/content/111/24…
Read 5 tweets

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