Facilitating analysis of genomic variation in Olympia oysters

This dataset includes genomic intervals (BED format) to facilitate RADSeq design and functional annotation of SNPs in Olympia oysters (<em>Ostrea lurida</em>). The files include a transcriptome (FASTA format) and the following 8 genomic interval files (BED format): <strong>Oly_snps_bed:</strong> location of SNPs with variant annotated in the name column<br><strong>Oly_geneID_bed:</strong> these intervals cover the entire length of the transcript and are annoated with the SwissProt ID in the name column<br><strong>Oly_regionofblasthits_bed:</strong> these intervals cover only the region of homology between the subject and query for the blastx output<br><strong>Oly_inducible_bed:</strong> these intervals cover the entire length of the transcript for those genes associated with the following GOSlim IDs: <em>cell-cell signaling, signal transduction, cell adhesion, development, stress response</em><br><strong>Oly_housekeeping_bed:</strong> these intervals cover the entire length of the transcript for those genes associated with the following GOSlim IDs: <em>DNA metabolism, RNA metabolism, protein metabolism</em><br><strong>Oly_EcoRIsites_bed:</strong> location of EcoRI restriction sites<br><strong>Oly_NotIsites_bed:</strong> location of NotI restriction sites<br><strong>Oly_SbfI_bed:</strong> 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:<br>Transcriptome characterization of the Olympia oyster and pinto abalone. Steven Roberts, Emma Timmins-Schiffman. figshare.<br>http://dx.doi.org/10.6084/m9.figshare.156431. Retrieved 18:14, Mar 18, 2013 (GMT)