nodalpoint.org - Neil's bioinformatics paper of the month - Comments

Cool does it for me

Neil — Fri, 08 Apr 2005 03:44:30 -0400

It's true that many people will overlook this, because (a) it doesn't involve medicine or humans and (b) it's in a fledgling and open access journal. Which is a shame. "Wow, that's cool" should be enough for any real scientist, IMHO.

I'm a big fan of the BMC journals (Bioinformatics, Genomics and Genome Biology).

re: dna preps

Neil — Fri, 08 Apr 2005 03:41:18 -0400

Presumably you get a bunch of fruit flies, gently mash them and extract DNA from the mess. If anything else is living inside the flies, you will get DNA from that too. How much of that DNA you end up cloning and sequencing then depends on the factors that you highlighted in the comment. Plasmid/E. coli DNA is screened out during the genome assembly (e.g. using cross_match).

I think this aspect of a sample containing DNA from other sources is one that people tend not to think about - which is one of the reasons that I found the paper of interest.

From the paper:"The amount of

Greg — Fri, 08 Apr 2005 03:26:07 -0400

From the paper:

"The amount of endosymbiont DNA present in a genome deposited in the Trace Archive depends on several factors: the number of sequences generated by the project, the size of the host genome, the size of the endosymbiont genome, and the number of copies of the endosymbiont present in each cell of the host."

I would now like to demonstrate my ignorance of DNA preparation techniques. Endosymbiont here refers to integrated Wolbachia DNA in the fruit fly DNA or fruit fly cell ? Does this mean the trace archive is picking up non-intracellular parasite/organismal DNA, or is that somehow excluded during the DNA extraction process ? Also how effective are the screens for plasmid/E. coli DNA ?

Marketing

Greg — Fri, 08 Apr 2005 03:18:21 -0400

It is quite impressive that mountains of data, full of potentially interesting discoveries, are just lying about in some NCBI server room. While the Wolbachia genomes study certainly demonstrates this, it just isn't marketable enough to spread the message. I'm only half joking here, I know that to the people that understand this stuff marketing is the last thing they would be thinking about. However it seems a shame that the "wow! that's kinda cool" aspect of this discovery (including the methods) will not be widely absorbed. I look forward to the next paper of the month, takers ?

Neil's bioinformatics paper of the month

Neil — Thu, 31 Mar 2005 18:17:26 -0500

As promised, it's April 1st and here's my publication pick. Published in February, so not exactly paper of the month, but not to worry. "Serendipitous discovery of Wolbachia genomes in multiple Drosophila species" by Salzberg et al. is in the open access journal Genome Biology, abstract here and full access here. Hit "read more" for the details.