Locate Plastid genes to add to euk marker set

gjospin / PhyloSift

Phylogenetic and taxonomic analysis for genomes and metagenomes

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Locate Plastid genes to add to euk marker set #155

Closed hollybik closed 12 years ago

hollybik commented 12 years ago

Jonathan's request...so that we can start pulling out Photosynthetic eukaryotes and cyanobacteria. The utility/issues associated with these markers will be similar to mitochondria

Cloroplast DB will be a good place to start - http://chloroplast.cbio.psu.edu/organism.cgi (probably will need to do a lot of file parsing and separating out marker genes into separate FASTA files - doesn't look like an easy way to download alignments for each gene...)

hollybik commented 12 years ago

Dongying has now run Markov clustering to get us some gene families - looks like we have about 200 of these for plastid genomes now. Sequences and alignments are on Merlot at:

/share/eisen/dwu/phylosift_marker_dir/chloro_family/chloro.family.tgz

gjospin commented 12 years ago

Plastid markers have been added to the DB.