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Facilitating analysis of genomic variation in Olympia oysters

Version 3 2013-03-18, 20:44
Version 2 2013-03-18, 20:44
Version 1 2013-03-18, 21:00
dataset
posted on 2013-03-18, 21:00 authored by Mackenzie GaveryMackenzie Gavery

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)

The original data for the transcriptome, blastx annotations and SNP tables can be found here:
Transcriptome characterization of the Olympia oyster and pinto abalone. Steven Roberts, Emma Timmins-Schiffman. figshare.
http://dx.doi.org/10.6084/m9.figshare.156431. Retrieved 18:14, Mar 18, 2013 (GMT)

 

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