Tag Archives: barcode

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Friday SNPpets

This week’s SNPpets include stories about the FlyBase memoriam for Bill Gelbart, Phenolyzer for gene discovery from phenotypes, tissue- and tumor-PPI comparison, Beacon, shotgun metagenomics, the future decade in genomics, no-so-scary personal genome sequencing and apps for it, DNA-barcoded beer, and more.


Welcome to our Friday feature link collection: SNPpets. During the week we come across a lot of links and reads that we think are interesting, but don’t make it to a blog post. Here they are for your enjoyment…


A Tree is Barcoded in Brooklyn

Figure 1 of the Plant Barcoding paperScrolling through some of my regular podcasts the other day I came across this tidbit about bioinformatics growing in New York (among other things, or course!):

Barcoding Plant DNA (I hope the embed of the audio file works, first time I’m trying that…)

It is a discussion with Dr. Damon Little, a curator of bioinformatics from the New York Botanical Garden.  The focus of the discussion is the recent publication of the CBOL Plant Working Group which has settled on the regions that will be used for barcoding plants.

If you aren’t familiar with barcoding efforts yet, you can check out Jennifer’s prior post with some background and great links.  Essentially a small snippet of DNA sequence is used to (hopefully) uniquely identify a given species.  This can be stored in a database–Dr. Little of the NY Botanical Garden refers to GenBank at NCBI, but there are other sites as well.  I was just reading about the web interface for barcoding called iBarcode.org for analyzing and managing this sort of data.

The Consortium for the Barcode Of Life Plant Working Group summary press release of this work can be found here.   The paper that describes the work is Open Access in PNAS here.  The paper describes the genes that had been candidates for the barcode, and the ones that were selected (rbcL + matK).  They described primer selection and sequencing results for the series they examined.  They evaluate which ones meet the barcoding standard criteria and provide the selections.  They use MUSCLE to examine the sequence alignments.

This is an excellent effort on many fronts.  Just assessing and cataloging biodiversity is useful itself, but this can also help to identify plants that are claimed to be used in food or medicine products to see if that is what’s really in there.  It can help combat poaching of protected species–for example, it can identify wood harvested that shouldn’t have been taken for lumber.

Glad to see this work moving forward and getting out in front of the public!

Related links

Podcast direct page: http://www.wnyc.org/shows/lopate/episodes/2009/07/29/segments/137623

NYBG: http://www.nybg.org/

Barcode blog: http://phe.rockefeller.edu/barcode/blog/

Scientific American article on the topic: http://www.scientificamerican.com/blog/60-second-science/post.cfm?id=botanists-agree-on-dna-barcode-for-2009-07-29

Consortium for the Barcode of Life (CBOL): http://www.barcoding.si.edu/

References
CBOL Plant Working Group (2009). A DNA barcode for land plants PNAS, 106 (31), 12794-12797 : 10.1073/pnas.0905845106

Singer, G., & Hajibabaei, M. (2009). iBarcode.org: web-based molecular biodiversity analysis BMC Bioinformatics, 10 (Suppl 6) DOI: 10.1186/1471-2105-10-S6-S14

Edgar, R. (2004). MUSCLE: multiple sequence alignment with high accuracy and high throughput Nucleic Acids Research, 32 (5), 1792-1797 DOI: 10.1093/nar/gkh340

Everyone may love a beagle, but I also like a BoLD project (update)

barcodeswan I recently met Karen James at the SBC. She is a scientist at The Natural History Museum, London and is also part of The HMS Beagle Project. That in itself is cool enough & I suggest you check out each of those entities, but in this blog I want to talk about something else she made me aware of: the Barcode of Life Data (BoLD) system. As I understand it, BoLD is a very cool data management system that allows the integration of DNA sequence data with its source specimen data for the documentation and analysis of both new and existing specimens in museum collections. Continue reading