facilitating analysis of genomic variation in olympia oysters
DESCRIPTION
Facilitating analysis of genomic variation in Olympia oysters. Bioinformatics, FISH546 Mackenzie Gavery 3/14/13. GOALS. U tilize existing genomic resources (transcriptome) for RAD- Seq design Generate useful generic feature files ( gff ) to facilitate functional annotation of SNPs - PowerPoint PPT PresentationTRANSCRIPT
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Facilitating analysis of genomic variation in Olympia oysters
Bioinformatics, FISH546Mackenzie Gavery3/14/13
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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*
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Methods
• Starting material:• Transcriptome: 41,000 contigs• SNP Table (CLCBio) ~52,000• Annotations: blastx, GO• Tools:• Galaxy• Excel• Blastx
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ResultsCut sites SNP w/in
50bpSNP w/in
100bp
NotI 118 43 64
SbfI 600 177 177
EcoRI 19,996 3,905 12,733
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Results
• New data tracks:• Gene ID• GO annotation sub-groups• SNPs• Blastx regions (with frame)
Cut sites SNP w/in 50bp
SNP w/in 100bp
NotI 118 43 64
SbfI 600 177 177
EcoRI 19,996 3,905 12,733
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Applications
• Assist with RAD-Seq experimental design• Ask interesting biological questions – are
there differences in the number of SNPs in housekeeping v. inducible genes?
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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)
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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