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Exposing the Machinery of the Resistome
aarondubrow writes "2011 Nobel Prize Winner, Bruce Beutler, is using the Ranger supercomputer at The University of Texas at Austin for an ambitious new project to discover all of the genes involved in the mammalian immune response – the so-called 'resistome.' Over several years, Beutler's lab will sequence the protein coding portions of genes in 8,000 mice to detect the impact of mutations on immunity. This means scanning, enriching and sequencing 500 billion base pairs every week. The project represents a 'Big Data' problem of the highest order."
The project represents a 'Big Data' problem of the highest order.
Before or after de-duplication of the data? Before, yes obviously but if that is still the case after de-duplication then gaining much knowledge from this experiment may prove to be a fools errand.
The genetic code has comments. Actually, it has something like a boot record for each gene. The gene part is called an Open Reading Frame (ORF) and it is marked by stop codons. The gene is the part of the DNA that is to be transcribed by RNA and then sent to the ribosomes, which are 3D protein printers. There are little switches that turn this process on and off for the different genes. Some of the genes, such as for metabolism, run all the time, others are for special occasions.
This was getting silly a few years ago with the metabolome. How many more omes (i.e. subsets of the total system that influences human biology) do we need to look at until we declare our human model complete? Is there going to be a 'humanome' that describes human-associated environmental factors? What about a 'radiatome' that describes the plethora of electromagnetic signals that enter our body over the course of a lifetime?
Ask me about repetitive DNA
As others have pointed out it is possible to deduce where genes are by looking at the sequence however this is by no means straightforward DNA is spaghetti code of the very worst kind.
It is possible to "run the DNA to see what it produces", basically when a (DNA) gene is active copy's of its sequence are made in messenger RNA (mRNA, its like DNA but much less stable) the mRNA copy's are perhaps akin to compiled code as there is a fair amount of rearrangement that goes on before its '3D printed' in protein.
Now its possible to take the mash up cells or tissue extract the mRNA convert it back to DNA (stabilising it) then sequence the different DNA molecules to find out what genes are active in a given tissue.
Mapping the sequences back to the genes is not straight forward, genes can exist in multiple identical or near identical copy's making it hard to map back, some genes never express or only express under very specific circumstances or only in certain people