De Novo Genome Analysis . . . . . Ketil Malde Analysis - PowerPoint PPT Presentation

De Novo . Institute of Marine Research Ketil Malde De Novo Genome Analysis . . . . . Ketil Malde Analysis Annotation evaluation Assembly Gene prediction Assembly Introduction October 2, 2012

De Novo . Annotation Assembly evaluation Gene prediction Assembly Introduction Overview . . . Ketil Malde . . Analysis Annotation evaluation Assembly Gene prediction Assembly Introduction Analysis

De Novo . 5. Annotate transcripts with function 4. Predict genes and transcripts 3. Build/train stochastic gene models (ESTs, RNAseq, proteins) 2. Map known sequences Processing a new genome . . . Ketil Malde . . Analysis Annotation evaluation Assembly Gene prediction Assembly Introduction 6. Do awesome biology stuff - yay! 1. Construct draft genome assembly

De Novo Ketil Malde Introduction Assembly Gene prediction Assembly evaluation Annotation Analysis . . . . . . e pipeline DNA sequences RNA sequences Genome assembly Related proteomes Gene T ranscript prediction assembly Assembled genome Genome evaluation Predicted transcriptome Annotation Annotated genes

De Novo Ketil Malde Introduction Assembly Gene prediction Assembly evaluation Annotation Analysis . . . . . . Assembly DNA sequences RNA sequences Genome assembly Related proteomes Gene T ranscript prediction assembly Assembled genome Genome evaluation Predicted transcriptome Annotation Annotated genes

De Novo . Ketil Malde . . . . . Assembly Analysis evaluation Assembly Gene prediction Assembly Introduction Annotation Shotgun reads Paired reads Contig assembly Overlaps: DeBruijn: - Celera/CABOG - ABYSS - Newbler - CLC - SRA Scaffolding Contigs - SSPACE - PCAP Scaffolded contigs

De Novo Ketil Malde Assembly . . . . . . Analysis Annotation evaluation Assembly Gene prediction Assembly Introduction Shotgun reads Contigs

De Novo . Assembly . . . . Ketil Malde . Analysis Annotation evaluation Assembly Gene prediction Assembly Introduction Shotgun reads Contigs Paired reads Scaffold

De Novo Ketil Malde Introduction Assembly Gene prediction Assembly evaluation Annotation Analysis . . . . . . Gene prediction DNA sequences RNA sequences Genome assembly Related proteomes Gene T ranscript prediction assembly Assembled genome Genome evaluation Predicted transcriptome Annotation Annotated genes

De Novo Ketil Malde Gene prediction . . . . . . Analysis Annotation evaluation Assembly Gene prediction Assembly Introduction Stochastic methods Scaffold

De Novo . Gene prediction . . . . Ketil Malde . Analysis Annotation evaluation Assembly Gene prediction Assembly Introduction RNA seq Training Stochastic methods RNA mapping Scaffold

De Novo . Gene prediction . . . Ketil Malde . . Analysis Annotation evaluation Assembly Gene prediction Assembly Introduction RNA seq Proteomes Training Stochastic methods Protein mapping RNA mapping Scaffold

De Novo . Gene prediction . . Ketil Malde . . . Analysis Annotation evaluation Assembly Gene prediction Assembly Introduction RNA seq Proteomes Training Stochastic methods Protein mapping RNA mapping Scaffold Gene model

De Novo Ketil Malde Introduction Assembly Gene prediction Assembly evaluation Annotation Analysis . . . . . . Assembly evaluation DNA sequences RNA sequences Genome assembly Related proteomes Gene T ranscript prediction assembly Assembled genome Genome evaluation Predicted transcriptome Annotation Annotated genes

De Novo . Assembly evaluation Ketil Malde . . . . . Analysis Annotation evaluation Assembly Gene prediction Assembly Introduction ◮ Accuracy ◮ read mapping scores ◮ Completeness ◮ mapped reads ◮ mapped proteins ◮ Fragmentation ◮ N50 etc. ◮ mapped pairs ◮ Redundancy ◮ total scaffold size ◮ multiply mapped reads ◮ mulitply mapped proteins

De Novo Ketil Malde Introduction Assembly Gene prediction Assembly evaluation Annotation Analysis . . . . . . Annotation DNA sequences RNA sequences Genome assembly Related proteomes Gene T ranscript prediction assembly Assembled genome Genome evaluation Predicted transcriptome Annotation Annotated genes

De Novo . Annotation . . . Ketil Malde . . Analysis Annotation evaluation Assembly Gene prediction Assembly Introduction Putative transcripts GO BLAST UniProt KEGG EC

De Novo . Transitive alignments . . . Ketil Malde . . Analysis Annotation evaluation Assembly Gene prediction Assembly Introduction r TGCA AGCT q p ACGT

De Novo Ketil Malde Introduction Assembly Gene prediction Assembly evaluation Annotation Analysis . . . . . . Awesome biology stuff!