Yesterday I set a goal for myself, BLAST the transcriptome against the sea urchin rather than the universal NCBI nt database. Spbase.org has an databases on sea urchin (echinodermata) RNA and protein, which would be informative to compare 1) contigs or 2) annotations to our sea stars spIDs. Suffice it to say, it was a struggle getting my script together and figuring out what monster I had decided to tackle. Here’s my code from the day, I am trying to repeat the BLAST today but this time against the genome (not a blastx) and with an Eval<-05.
August 12 Sea Urchin BLAST notebook:
I spent some time during the blast playing around with our enriched processes from DAVID. Thoughts on GO terms- DAVID outputs a multitude of GO terms with our spIDs but PANTHER, another gene ontology software, seems to parse down the number of GO terms. Not that this is changing the annotations, but it might be useful when looking at the overall changes in metabolic process.