Neanderthal Genome is Finished and Free
March 21, 2013 8:11 AM
comment(s) - last by
DNA comes from sequencing of Neanderthal toe-bone found in Siberia
Three years after an international team of experts led by researchers at the
Max Planck Institute for Evolutionary Anthropology
in Leipzig, Germany published a
"draft" of the genome of
(commonly known as the "Neanderthal"), the team has
with a higher-quality "finished" map of the genome.
I. Getting to Know Our Neighbors, Distant Ancestors
Neanderthals are one of mankind's closest relatives. Neanderthals and modern man (
) are though to have diverged from a common ancestor around 350,000 years ago. That ancestor is thought to have evolved into humans in Africa, but into Neanderthals in Europe. Another close relative, Denisovans, are thought to have diverged slightly earlier in Asia.
Nonetheless, humans and these relatives would eventually reunite and even have
intimate sexual relationships
, which led to some modern humans bearing pieces of Neanderthal/Denisovan DNA.
These "donations" from our close relatives are thought to have endowed people of European or Asian descent with hardier immune systems.
The DNA for the sequenced Neanderthal genome comes from a toe-bone found in the Denisova cave in southern Siberia.
[Image Source: Current Biology/Science]
That cave is also home to preserved human and Denisovan remains; in fact the Denisovan remains are being used to carry out a similar sequencing project on that genome.
II. Contamination, Region Variance Leave Picture Only Mostly Complete
, a geneticist who led the research, wrote in
, "The genome of a Neanderthal is now there in a form as accurate as that of any person walking the streets today."
Or it is for the Altal Neanderthals, at least. Much like modern man, where people from different areas developed unique genetic makeups, Neanderthals are hypothesized to have subtle regional differences in their genomes.
, it is misleading to suggest that the genome is a "complete" genome for the entirety of the Neanderthal population that once inhabited Europe, Asia, and the Middle East. Rather, the Neanderthal genome represents a finished/complete picture of the Neanderthals in
Scientists think that the Altal branch of the "family tree" is complete with the finished sequencing. [Image Source: MPI]
Professor Paabo is preparing a paper on the work. He enthuses, "We will gain insights into many aspects of the history of both Neanderthals and Denisovans, and refine our knowledge about the genetic changes that occurred in the genomes of modern humans after they parted ways with the ancestors of Neanderthals and Denisovan."
The finished genome is
in "BAM" format, with chromosome file sizes ranging from 1.9-13 GB a piece, depending on the size, except for the small 'Y' chromosome, which is only 331 MB.
One other way that the genome is somewhat incomplete is contamination. Analysis showed that approximately 1 percent of the DNA in the sample was contamination from the cave's later human residents. Those gaps -- and the variations between Neanderthals in different regions -- will have to be filled in with future gene studies.
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RE: What kind of idiotic file format...
3/21/2013 1:06:28 PM
3.2 billion base pairs is actually 3.2 billion bits.
Since effectively the data is RAND compression is highly unlikely to save many bits
3.2 /8 = 400 million bytes. He was correct in his 400mb size file.
Unless there is 'empty pairs' of sorts. There is no need for vertexes if you run sequential.
Now given if there is variable count per specie (I am no genetitsist (sp?)) then the solution is simply count til finished
You only need to run a tree if there is a variable placement based upon previous results and then only if the system is not self indexing.
RE: What kind of idiotic file format...
3/21/2013 6:40:18 PM
I would imagine there is a bunch of extra information to allow the data to be accessed / searched faster, such as what proteins various sections lead to , and possibly a index column that says what numerical position each base pair is in. Im no expert on databases though, but there are plenty of retarded ways to make databases, and although text files of pure data are nice and small they take forever to search.
"It seems as though my state-funded math degree has failed me. Let the lashings commence." -- DailyTech Editor-in-Chief Kristopher Kubicki
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