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ANSC644 Bioinformatics

ANSC644 Bioinformatics. Carl J. Schmidt 051 Townsend Hall schmidtc@udel.edu http://udgenome.ags.udel.edu/ANSC644. Bioinformatics. Application of computer science to aid the life scientist in understanding biological processes. Bioinformatics.

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ANSC644 Bioinformatics

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  1. ANSC644 Bioinformatics • Carl J. Schmidt • 051 Townsend Hall • schmidtc@udel.edu • http://udgenome.ags.udel.edu/ANSC644 ANSC644 Bioinformatics-Database Mining

  2. Bioinformatics • Application of computer science to aid the life scientist in understanding biological processes. ANSC644 Bioinformatics-Database Mining

  3. Bioinformatics • Application of computer science to aid the life scientist in understanding biological processes. Computer Science Life Science ANSC644 Bioinformatics-Database Mining

  4. Bioinformatics • Application of computer science to aid the life scientist in understanding biological processes. Computer Science Life Science Statistics ANSC644 Bioinformatics-Database Mining

  5. Objectives: • Introduce web accessible bioinformatics programs ANSC644 Bioinformatics-Database Mining

  6. Objectives: • Introduce web accessible bioinformatics programs • Perspective of the life scientist ANSC644 Bioinformatics-Database Mining

  7. Objectives: • Introduce web accessible bioinformatics programs • Perspective of the life scientist • What is available? ANSC644 Bioinformatics-Database Mining

  8. Objectives: • Introduce web accessible bioinformatics programs • Perspective of the life scientist • What is available? • How do I use these tools? ANSC644 Bioinformatics-Database Mining

  9. Objectives: • Introduce web accessible bioinformatics programs • Perspective of the life scientist • What is available? • How do I use these tools? • What do the results mean? ANSC644 Bioinformatics-Database Mining

  10. Mining Internet Biomedical Databases

  11. Database • A computer accessible organized source of information. Three types- differ in how data is organized. ANSC644 Bioinformatics-Database Mining

  12. Database • A computer accessible organized source of information. Three types- differ in how data is organized. • Flatfile- ordered collection of files, typically in a standard format. ANSC644 Bioinformatics-Database Mining

  13. Database • A computer accessible organized source of information. Three types- differ in how data is organized. • Flatfile- ordered collection of files, typically in a standard format. • Relational Database-Information is stored in a collection of tables. ANSC644 Bioinformatics-Database Mining

  14. Database • A computer accessible organized source of information. Three types- differ in how data is organized. • Flatfile- ordered collection of files, typically in a standard format. • Relational Database-Information is stored in a collection of tables. • Object Oriented Database-Can handle complex objects, beyond tables (images, video files) ANSC644 Bioinformatics-Database Mining

  15. Database • A computer accessible organized source of information. Three types- differ in how data is organized. • Flatfile- ordered collection of files, typically in a standard format. • Relational Database-Information is stored in a collection of tables. • Object Oriented Database- Can handle complex objects beyond tables such as images, video files etc. ANSC644 Bioinformatics-Database Mining

  16. Some Relationships for a Given Gene GENE ANSC644 Bioinformatics-Database Mining

  17. Some Relationships for a Given Gene Sequence GENE ANSC644 Bioinformatics-Database Mining

  18. Some Relationships for a Given Gene Sequence GENE Publications ANSC644 Bioinformatics-Database Mining

  19. Some Relationships for a Given Gene Sequence GENE Publications Product Publications Structure ANSC644 Bioinformatics-Database Mining

  20. Some Relationships for a Given Gene Homologs Sequence GENE Publications Product Publications Structure ANSC644 Bioinformatics-Database Mining

  21. Some Relationships for a Given Gene Homologs Sequence GENE Publications Expression Data Product Publications Structure ANSC644 Bioinformatics-Database Mining

  22. Some Relationships for a Given Gene Homologs Sequence GENE Publications Expression Data Mutation Data Product Phenotype Publications Structure ANSC644 Bioinformatics-Database Mining

  23. Entrez • Central Query Page for Biomedical Information. • Includes: • Literature • Sequences • Nucleotide • Protein • Structures • Online Mendelian Inheritance in Man • Much more ANSC644 Bioinformatics-Database Mining

  24. Entrez • Query interface Pubmed - literature Entrez Query Page DBs Nucleotide Sequences Online Mendelian Inheritance ANSC644 Bioinformatics-Database Mining

  25. Link ANSC644 Bioinformatics-Database Mining

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  29. Boolean operators • The search engine understands: • AND, OR, NOT • This permits refining the search to focus on topic of interest. • If no operated added PUBMED uses AND between terms. • Virus infection is {Virus AND infection} ANSC644 Bioinformatics-Database Mining

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  43. PUBMED Tutorial ANSC644 Bioinformatics-Database Mining

  44. Pubcrawler ANSC644 Bioinformatics-Database Mining

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