GENOMICS COMPUTATIONAL · 2018. 4. 24. · ST43 ST418 ST3g-2LV ST37-1LV ST 37 ST36 ST340-1LV ST340...
Transcript of GENOMICS COMPUTATIONAL · 2018. 4. 24. · ST43 ST418 ST3g-2LV ST37-1LV ST 37 ST36 ST340-1LV ST340...
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COMPUTATIONAL GENOMICS
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Genome Assembly
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De Novo vs Reference Assembly
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Consistency of De Novo Assembly
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Choice of Assembler
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Assembly Quality Comparison
SkesaSpadesUnicyclerMaSuRCA
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Genome Assembly Pipeline
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Gene Prediction &
Functional Annotation
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Objectives
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Merge
Merge
Merge
Gene Prediction Pipeline
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Gene Prediction Results
Coding Regions Non coding Regions
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Functional Annotation Pipeline
gff
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Signal Peptides: SignalP-4.1
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Lipoproteins and TM Proteins: LipoP
Genome
No. of Hits
Avg: 967 genes per genome
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Genome
No. of Hits
Operons: DOOR2
Avg: 280 genes per genome
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eggNOG-mapper
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CRISPR: PILER-CRTotal 84 hits among 50 genomes
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Prophage: PHASTER (PHAge Search Tool Enhanced Release)
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Antibiotic Resistance: RGI
Avg: 43 genes per genome
Fosfomycin inactivating enzyme (FosA5 or FosA6) present in all the genomes
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Virulence Factors: VFDB + Victor
Genome
No. of Hits
SRR4017925 Avg: 36 genes per genome
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Comparative Genomics
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Comparative Genomics Pipeline
Predict
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ST258
Similarity Analysis
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Presence or Absence of Genes
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Intergenic Regions
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Multilocus Sequence Typing
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HeteroresistantResistantSusceptible
kSNP3.0
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Conclusion?
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Predictive Web Server Demo
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Extra Slides
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Gene Prediction Results - BLAST+ Results%
Bla
st H
its
SRR5666568
SRR5666568
Coding Regions Non-Coding Regions