Comparative Genomics Comparative Genomics Common Themes Gene and - - PowerPoint PPT Presentation

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Comparative Genomics Comparative Genomics Common Themes Gene and - - PowerPoint PPT Presentation

Feb 22, 2024 325 likes •496 views

Comparative Genomics Comparative Genomics Common Themes Gene and functional pathway presence/absence Identification, alignment of orthologs Structural analysis and comparison Comparative Genomics Basic Local Alignment Search Tool

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SLIDE 1

Comparative Genomics

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SLIDE 2

Comparative Genomics

Common Themes

  • Gene and functional pathway presence/absence
  • Identification, alignment of orthologs
  • Structural analysis and comparison
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SLIDE 3

Comparative Genomics

Basic Local Alignment Search Tool (BLAST)

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SLIDE 4

Comparative Genomics

The Core BLAST Programs

Program Query Sequences Database Sequences Alignment blastn nucleotide nucleotide nucleotide blastp amino acid amino acid amino acid blastx nucleotide amino acid amino acid tblastn amino acid nucleotide amino acid tblastx nucleotide nucleotide amino acid

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SLIDE 5

Comparative Genomics

Downstream Applications

  • Identify orthologs
  • Reciprocal BLAST
  • OrthoMCL
  • Annotation and Pathway Analysis
  • e.g., BLAST2GO
  • Many others
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SLIDE 6

Comparative Genomics

Advantages of Running BLAST Locally

  • Customize databases with unpublished sequences
  • Run thousands of simultaneous searches
  • Integrate into custom scripts and pipelines
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Comparative Genomics

Parsing BLAST Output

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SLIDE 8

Comparative Genomics

Organization of BLAST Output

  • RESULTS – One results block for each sequence in the
  • riginal query file
  • HITS – Within each results block, one hit block for

each sequence in the database that produced a significant alignment

  • HSPs – Within each hit block, one high-scoring-

pair block for each significant local alignment to that hit

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SLIDE 9

Comparative Genomics

Parsing BLAST Output

http://bioperl.org/howtos/SearchIO_HOWTO.html

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SLIDE 10

Comparative Genomics

Parsing BLAST Output – BioPerl Results Information

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SLIDE 11

Comparative Genomics

Parsing BLAST Output – BioPerl Hit Information

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SLIDE 12

Comparative Genomics

Parsing BLAST Output – BioPerl HSP Information

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SLIDE 13

Comparative Genomics

Parsing BLAST Output – BioPerl HSP Information (Cont.)

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SLIDE 14

Exercise

  • Make BLAST databases
  • Run local BLAST searches
  • Parse BLAST output with BioPerl
  • Make dot-plot comparing two bacterial genomes in R using parsed BLAST
  • utput

https://dbsloan.github.io/TS2019/exercises/local_blast.html