61–70 of 232 posts
Does this literally mean every single base pair with all the junk genome and everything else? Or is it some statistical model/extrapolated etc.
Could someone explain exactly what it means to be "completely sequence" the human genome when all humans have distinct genetic makeup (ie, different sequences of nucleobases in their DNA/RNA)?
Ideally we'd have hundreds if not thousands of complete genomes which in total would reveal the population diversity of the human species as it currently exists, but this is a big ask. "Clincal variants" are of particular interest as those are regions of the genome associated with certain inherited diseases, although the promises of individual genomic knowledge leading to a medical revolution have turned out to be wildly overblown.
Since the paper is paywalled, there's not much else to say than that they have a (fairly arbitrary in origin, i.e. it could have been from any one individual or possibly even a chimera of several individuals) reference sequence to which other specific human Y chromosomes can be compared, eventually leading to a larger dataset from many individuals which will reveal the highly conserved and highly variable regions of the chromosome, population-wise.
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Yes, but the HGP didn't make a full sequence either, using their scaffold-based contig assembly. Both groups declared a truce and announced they were "finished with the first draft" 35 years ago: https://www.nytimes.com/1987/12/13/magazine/the-genome-proje... 33 years ago: https://www.nytimes.com/1990/06/05/science/great-15-year-pro... 29 years ago: the competition gets fierce https://www.nytimes.com/1994/02/22/scien…
Lets not forget how Perl Saved The Human Genome Project [1], which I remember seeing in a print magazine at the time. As someone who is in the genomics world now as a software person, I find it amusing that I've gotten more into perl over the last year or so. It has its place, in the way that grep/sed/awk/etc does. [1] https://news.ycombinator.com/item?id=30327812
IMHO the person who "saved the genome project" was WJ Kent, who developed the assembler, BLAT, that the public project needed. I strive to point out that he wasn't a sole hero, nor was Lincoln. What I really like about BLAT is that while Celera was using Big Iron UNIX (massive 64-bit 64GB machines with 10s of terabytes of central high performance storage), BLAT ran on a cluster of linux machines, right around the time that people were waking up to the fact that linux was becoming a useful tool for scientific data processing. BLAT's design allowed it to work on a cluster of cheaper/smaller machines, while celera's algorithm really needed a massive shared memory single machine. it was sort of a microcosm of the larger battle being fought between Big iron UNIX and little intel linux at the time.
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It's a slight exaggeration of the information content to report the data size using an ASCII encoding. Since there are 4 bases, each can be encoded using 2 bits, rather than 8. So we're really talking 750 megabytes. But still mind-blowing.
Yes, and if you gzip it it's even smaller. But the big takeaway is that the amount of info that fully defines a human, is what we consider "not much data," even in its plainest encoding.
Since genome files contain more data than just ATGC (typically a comment line, then a DNA line, then a quality score line), and each of those draws from a different distribution, DEFLATE on a FASTA file doesn't reach the full potential of the compressor because the huffman table ends up having to hold all three distributions, and the dictionary backlookups aren't as efficient either. It turns out you can split the file into multiple streams, one per line type, and then compress those independently, with slightly better compression ratios, but it's still not great.
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> That is if we transfer the DNA to an advanced alien civilization - would they be able to make a human. You'd need a cell to start the process, with the various nucleic acids distributed correctly and proteins/energy with which to create further proteins using the information encoded by the DNA. Thus the civilization would need information about cells and a set of building blocks before being able to use the DNA.
The DNA contains all the code that creates and regulates the proteins.
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This is a complex question. The cocktail soup in a gamete (sperm or egg) and the resulting zygote contains an awful lot of stuff that would be extremely hard to replace. I could imagine that if the receiving civilization was sufficiently advanced and had a model of what those cells contained (beyond the genomic information) they could build some sort of artificial cell that could bootstrap the genome to the point of…
The code how to build a sperm and an egg is inside the human DNA, isn't it?
This is actually kind of a huge deal since it means that all 24 chromosomes have now been fully sequenced. As it says in the abstract, up until now the Y chromosome proved difficult to sequence due to its nature.
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Lets not forget how Perl Saved The Human Genome Project [1], which I remember seeing in a print magazine at the time. As someone who is in the genomics world now as a software person, I find it amusing that I've gotten more into perl over the last year or so. It has its place, in the way that grep/sed/awk/etc does. [1] https://news.ycombinator.com/item?id=30327812
Lincoln Stein is great, and perl was certainly critical to many processes, but it was and remains fairly niche in genomics, which used much more C++, Java, and later Python. IMHO the person who "saved the genome project" was WJ Kent, who developed the assembler, BLAT, that the public project needed. I strive to point out that he wasn't a sole hero, nor was Lincoln. What I really like about BLAT is that while Celera w…
Earlier quoted context omitted.
Lets not forget how Perl Saved The Human Genome Project [1], which I remember seeing in a print magazine at the time. As someone who is in the genomics world now as a software person, I find it amusing that I've gotten more into perl over the last year or so. It has its place, in the way that grep/sed/awk/etc does. [1] https://news.ycombinator.com/item?id=30327812
Lincoln Stein is great, and perl was certainly critical to many processes, but it was and remains fairly niche in genomics, which used much more C++, Java, and later Python. IMHO the person who "saved the genome project" was WJ Kent, who developed the assembler, BLAT, that the public project needed. I strive to point out that he wasn't a sole hero, nor was Lincoln. What I really like about BLAT is that while Celera w…
However, I got into the genomics world in the early aughts, and the perl hung on and on and on. I remember starting a new job in the mid-teens, and one of the first tasks I had was to port over a legacy perl script. Such is the world of scientific software. 99% of the people I know who have touched perl since ~2003ish are in the bioinformatics space.
This is actually kind of a huge deal since it means that all 24 chromosomes have now been fully sequenced. As it says in the abstract, up until now the Y chromosome proved difficult to sequence due to its nature.