After six months of working on this project, I’ve amassed a collection of over 5,500 sequences from lichen photobionts and their relatives. Storage and retrieval of this data using text files has become increasingly unwieldy for me, and I suspect that very few other people have been bothering to access the github repository where the data are archived. In an effort to improve accessibility, I’ve migrated this blog to a dedicated web server and created a searchable SQL database that can be accessed right from the blog. Below the banner, you’ll find a “Photobiont Sequences” tab, that will allow you to select green algae or cyanobacteria, specific genes, or the entire database. You can search for specific photobiont or host species, or filter the table using the selection boxes below each column.
My hope is that people who are interested in a particular group of lichens can use these tables to find out what photobiont(s) they are associated with. This information is not consistently encoded in Genbank, so until now it has usually required a laborious literature search to obtain it. Please let me know if you find this to be useful and if there are additional enhancements that you would like to see. I will be adding high-resolution trees for each group in the coming weeks, and hope to make them searchable as well if I can overcome the technical challenges of doing so. I’m also hoping to add links to Genbank for all of the sequences in the database.
Enjoy!
Heath OBrien (2013). PhotobiontDiversity.org: a searchable database of photobiont sequences PhotobiontDiversity.org : http://dx.doi.org/10.6084/m9.figshare.841758
I can’t search for or click on any of the taxa in your database. What am I missing???
There should be a search field above the table and at the bottom of each column. If not it’s probably a problem with jquery. I will have to figure out some useful fall-back for when that doesn’t work. It’s true that clicking doesn’t do anything useful. I need to add hyperlinks to the sequences but I’ve been to busy/lazy to get to it
Heath: this is a great blog for a specialist. You can go here and get data, some bits of information about the methods, and an in-depth discussion of results. Even seems citable! Great open publishing concept.
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