Genome assembly, repeats, and reading the genome, Jim Kent
Interviewee: Jim Kent. Jim Kent, the author of the assembly program for the public sequence, talks about the difficulties of reassembling small pieces of the genome when there are so many repeat sequences.
The problem of genome assembly is basically that we can only read small bits of the genome, and the way we do it is we'll typically just read a random small bit. And so, to see the whole thing, we've got to stitch it together from these random little reads. And in principle this wouldn't be too hard except for the fact that the genome is not really like a book, it's not like prose, it's more like poetry. It has a lot of repeating elements. And when you get in a repeating elements you can actually get a bit lost when you're trying to stitch it together.
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Jim Kent talks about the data structure of the human genome: poetry or prose?
Jim Kent talks about the difficulties of DNA assembly.
Jim Kent talks about dealing with sequencing data.
Jim Kent, the author of the assembly program for the public sequence, talks about the challenge of reassembling the genome.
Jim Kent talks about a farm of computers.
Jim Kent talks about transposons and repetitive elements in the human genome.
Jim Kent talks about cell division and DNA.
James Watson describes sequencing the human genome using markers and BACs, and Craig Venter explains using cDNA libraries, ESTs, and shotgun sequencing.
Jim Kent talks about telomeres and cell death.
Jim Kent talks about junk DNA in the human genome.