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  • Mean 611 bp
  • Putting them on a wiki - ..8 cutters, and a 6 cutterApplications: SNPs per base pair for different functional groupsOther combinations of data: CpG ratios
  • Putting them on a wiki - ..8 cutters, and a 6 cutterApplications: SNPs per base pair for different functional groupsOther combinations of data: CpG ratios

Fish546 Fish546 Presentation Transcript

  • Facilitating analysis ofgenomic variation inOlympia oystersBioinformatics, FISH546Mackenzie Gavery3/14/13
  • GOALS• Utilize existing genomic resources (transcriptome) for RAD-Seq design• Generate useful generic feature files (gff) to facilitate functional annotation of SNPs• Generate a workflow for annotating synonymous and non-synonymous SNPs in a non-model species*
  • Methods• Starting material: • Transcriptome: 41,000 contigs • SNP Table (CLCBio) ~52,000 • Annotations: blastx, GO• Tools: • Galaxy • Excel • Blastx
  • Results Cut sites SNP w/in SNP w/in 50bp 100bp NotI 118 43 64 SbfI 600 177 177 EcoRI 19,996 3,905 12,733
  • Results Cut sites SNP w/in SNP w/in 50bp 100bp NotI 118 43 64 SbfI 600 177 177 EcoRI 19,996 3,905 12,733• New data tracks: • Gene ID • GO annotation sub-groups • SNPs • Blastx regions (with frame)
  • Applications• Assist with RAD-Seq experimental design• Ask interesting biological questions – are there differences in the number of SNPs in housekeeping v. inducible genes?
  • Next steps• Do these SNPs result in functional changes (i.e. do they change the protein)?1. Blastx custom output -outfmt “6 sseqid, qseqid, frames…”2. aachanges (Galaxy)
  • Next steps• Do these SNPs result in functional changes (i.e. do they change the protein)?1. Blastx custom output -outfmt “6 sseqid, qseqid, frames…”2. aachanges (Galaxy) SNP bed gene bed