A new fileset was just published that provides new insights into Olympia oyster genomics.
Facilitating analysis of genomic variation in Olympia oysters
Mackenzie Gavery. figshare
This along with other filesets from FISH546 are featured at oystergen.es/fish546
This dataset includes genomic intervals (BED format) to facilitate RADSeq design and functional annotation of SNPs in Olympia oysters (Ostrea lurida).
The files include a transcriptome (FASTA format) and the following 8 genomic interval files (BED format):
Oly_snps_bed: location of SNPs with variant annotated in the name column
Oly_geneID_bed: these intervals cover the entire length of the transcript and are annoated with the SwissProt ID in the name column
Oly_regionofblasthits_bed: these intervals cover only the region of homology between the subject and query for the blastx output
Oly_inducible_bed: these intervals cover the entire length of the transcript for those genes associated with the following GOSlim IDs: cell-cell signaling, signal transduction, cell adhesion, development, stress response
Oly_housekeeping_bed: these intervals cover the entire length of the transcript for those genes associated with the following GOSlim IDs: DNA metabolism, RNA metabolism, protein metabolism
Oly_EcoRIsites_bed: location of EcoRI restriction sites
Oly_NotIsites_bed: location of NotI restriction sites
Oly_SbfI_bed: location of SbfI restriction sites
This dataset was generated as part of the requirements for FISH 546: Bioinformatics for Environmental Science. The slides for the final presentation are included (FISH546.pdf)