Gas station without pumps

2011 February 7

World’s largest genome?

Filed under: Uncategorized — gasstationwithoutpumps @ 11:20
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The Scientist has just published a news article, Jaume and the Giant Genome, which announces the existence of a 150 gigabase genome.  Not surprisingly, this huge genome is in a plant, “the Japanese canopy plant (Paris japonica), native to the mountains surrounding Nagano.” The genome size was measured at Kew Gardens, which has a huge repository of diverse plants (perhaps 12% of the known plant species).

I doubt that anyone will be rushing to sequence such a huge genome (50 times larger than the human genome).  I wonder how long it will be before someone discovers a still longer plant genome.

2011 January 31

The Assemblathon

Filed under: Uncategorized — gasstationwithoutpumps @ 03:35
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There is a new bioinformatics contest: The Assemblathon.  The idea is to provide a CASP-like competition for judging the quality of genome assembly methods from next-generation sequence data.

Actually there are two contests, the Assemblathon and the de Novo Genome Assessment Project (dnGASP), which is based in Europe.

I’ve been thinking that I ought to be entering the Assemblathon, since genome assembly is one of the fields I’m planning to investigate for my sabbatical, but I have no software for assembling Illumina reads (or simulations of them, which is what the Assemblathon is using).  The deadline for submitting assemblies is Feb 6, so there is certainly no time for developing new software (even if I had time for research with my teaching load this year). My main interest is in small genomes (prokaryotes), but the Assemblathon is focused on diploid genomes about the size of a human chromosome.

Of course, the results of the Assemblathon will be coming out just in time for the Banana Slug Genomics class this spring, and we’ll certainly be looking at the results very carefully and trying to get our hands on the software that performs best, because the banana slug genome is probably at least as difficult as the Assemblathon pseudo-genome.  (It may be polyploid and it is almost certainly bigger than one human chromosome.)


2010 December 24

23andme poetry contest

Filed under: Uncategorized — gasstationwithoutpumps @ 18:16
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The personalized medicine company 23andme is sponsoring a poetry competition: The Spittoon » Are You A Poet? Let Us Know It (and Win a Prize). The contest requires a poem (in any style) using at least 5 words or phrases from their list.  The prizes are tickets to PMWC 2011 January 18–19, 2011 at the Computer History Museum in Mountain View, CA.

I used to fancy myself a poet (about 30–40 years ago), but I haven’t found their word list very inspiring. Of course, I don’t find 23andme’s SNP-based sequence analysis very inspiring either. I suspect that most of the interesting things in my genome (if there are any interesting things) are idiosyncratic mutations that are just found in me and a few close relatives, and so are inaccessible to the common-haplotype approach of 23andme.

I’m still waiting for the under $1000 genome—maybe then I’ll get my personal genome.

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