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heathobrien
I am a genome scientist based in Bristol, England. I am currently studying the genetic basis of neuropsychiatric disorders, but I have also done research on iridescent plants, plant pathogens and lichens. I have continued my work on lichen-associated algae and cyanobacteria for my blog
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Algae Anabaena Asterochloris Azolla Cladonia Cladoniaceae Coccomyxa Cyanobacteria database Degelia Dothideomycetes Eurotiomycetes genbank Green algae gunnera Introduction ITS Lepraria Lichen Methods Nostoc omphalina Paramecium Peltigera Peltigerales Phylogenetics plant symbiosis Pyrenula reproductive mode Rhizonema Scytonema sql Stereocaulaceae Trebouxia Trentepohliales XanthoriaBlogRoll
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Tag Archives: Methods
Adding new sequences (Mistakes were made)
Looking through the tree produced in my last post, I noticed that several interesting sequences were missing from the tree. There are also less sequences in the tree than I get if I search for “Nostoc rbcX” in Entrez. Turns … Continue reading
Adding host information to the Nostoc phylogeny
Having obtained 496 Nostoc rbcX sequences (plus one outgroup) and used them to infer a reasonable phylogeny, all that is left is to assign host association information to the branches. This will require (a) parsing the sequence files to obtain host … Continue reading
Obtaining the sequences
Perhaps not surprisingly given my background, I will be starting with Nostoc photobionts. In my opinion, the most useful marker for this group is rbcX, so I will be starting there. I have decided to use blast to obtain all … Continue reading
