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De Novo Ketil Malde Introduction Assembly Gene prediction Assembly evaluation Annotation Analysis
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De Novo Ketil Malde Introduction Assembly Gene prediction Assembly evaluation Annotation Analysis
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De Novo Genome Analysis . . . . . Ketil Malde Analysis - - PowerPoint PPT Presentation
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
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De Novo Ketil Malde Introduction Assembly Gene prediction Assembly evaluation Annotation Analysis
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Processing a new genome
- 1. Construct draft genome assembly
- 2. Map known sequences
(ESTs, RNAseq, proteins)
- 3. Build/train stochastic gene models
- 4. Predict genes and transcripts
- 5. Annotate transcripts with function
- 6. Do awesome biology stuff - yay!
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De Novo Ketil Malde Introduction Assembly Gene prediction Assembly evaluation Annotation Analysis
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e pipeline
DNA sequences RNA sequences Assembled genome Genome assembly Predicted transcriptome Gene prediction T ranscript assembly Genome evaluation Related proteomes Annotated genes Annotation
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De Novo Ketil Malde Introduction Assembly Gene prediction Assembly evaluation Annotation Analysis
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Assembly
DNA sequences RNA sequences Assembled genome Genome assembly Predicted transcriptome Gene prediction T ranscript assembly Genome evaluation Related proteomes Annotated genes Annotation
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De Novo Ketil Malde Introduction Assembly Gene prediction Assembly evaluation Annotation Analysis
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Assembly
Shotgun reads Paired reads Contig assembly
Overlaps:
- Celera/CABOG
- Newbler
DeBruijn:
- ABYSS
- CLC
- SRA
Contigs Scaffolding
- SSPACE
- PCAP
Scaffolded contigs
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De Novo Ketil Malde Introduction Assembly Gene prediction Assembly evaluation Annotation Analysis
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Assembly
Shotgun reads Contigs
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De Novo Ketil Malde Introduction Assembly Gene prediction Assembly evaluation Annotation Analysis
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Assembly
Shotgun reads Contigs Paired reads Scaffold
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De Novo Ketil Malde Introduction Assembly Gene prediction Assembly evaluation Annotation Analysis
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Gene prediction
DNA sequences RNA sequences Assembled genome Genome assembly Predicted transcriptome Gene prediction T ranscript assembly Genome evaluation Related proteomes Annotated genes Annotation
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De Novo Ketil Malde Introduction Assembly Gene prediction Assembly evaluation Annotation Analysis
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Gene prediction
Stochastic methods
Scaffold
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De Novo Ketil Malde Introduction Assembly Gene prediction Assembly evaluation Annotation Analysis
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Gene prediction
Stochastic methods
Scaffold
RNA mapping
RNA seq
Training
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De Novo Ketil Malde Introduction Assembly Gene prediction Assembly evaluation Annotation Analysis
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Gene prediction
Stochastic methods
Scaffold
RNA mapping
RNA seq
Training Protein mapping
Proteomes
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De Novo Ketil Malde Introduction Assembly Gene prediction Assembly evaluation Annotation Analysis
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Gene prediction
Stochastic methods
Scaffold
RNA mapping
RNA seq
Training Protein mapping
Proteomes Gene model
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De Novo Ketil Malde Introduction Assembly Gene prediction Assembly evaluation Annotation Analysis
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Assembly evaluation
DNA sequences RNA sequences Assembled genome Genome assembly Predicted transcriptome Gene prediction T ranscript assembly Genome evaluation Related proteomes Annotated genes Annotation
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De Novo Ketil Malde Introduction Assembly Gene prediction Assembly evaluation Annotation Analysis
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Assembly evaluation
◮ Accuracy
◮ read mapping scores
◮ Completeness
◮ mapped reads ◮ mapped proteins
◮ Fragmentation
◮ N50 etc. ◮ mapped pairs
◮ Redundancy
◮ total scaffold size ◮ multiply mapped reads ◮ mulitply mapped proteins
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De Novo Ketil Malde Introduction Assembly Gene prediction Assembly evaluation Annotation Analysis
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Annotation
DNA sequences RNA sequences Assembled genome Genome assembly Predicted transcriptome Gene prediction T ranscript assembly Genome evaluation Related proteomes Annotated genes Annotation
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De Novo Ketil Malde Introduction Assembly Gene prediction Assembly evaluation Annotation Analysis
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Annotation
Putative transcripts BLAST GO KEGG EC UniProt
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De Novo Ketil Malde Introduction Assembly Gene prediction Assembly evaluation Annotation Analysis
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Transitive alignments
AGCT
p q
r
ACGT TGCA
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De Novo Ketil Malde Introduction Assembly Gene prediction Assembly evaluation Annotation Analysis
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