1 / 35

Demo: Protein Information Resource

Demo: Protein Information Resource. March 28, 2002 NIH Proteomics Workshop Bethesda, MD Lai-Su Yeh, Ph.D. Protein Scientist, National Biomedical Research Foundation. Database Demo. NREF Database http://pir.georgetown.edu/pirwww/search/pirnref.shtml iProClass Database

Télécharger la présentation

Demo: Protein Information Resource

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.


Presentation Transcript

  1. Demo: Protein Information Resource March 28, 2002 NIH Proteomics Workshop Bethesda, MD Lai-Su Yeh, Ph.D. Protein Scientist, National Biomedical Research Foundation

  2. Database Demo • NREF Database • http://pir.georgetown.edu/pirwww/search/pirnref.shtml • iProClass Database • http://pir.georgetown.edu/iproclass.html • iProClass Sequence (A58910), Motif (PCM00487) • PIR-PSD Database • http://pir.georgetown.edu/cgi-bin/pirwww/nbrfget?&uid=A58910 • PIR Entry (A58910) • Other Molecular Databases • Function: KEGG Enzyme (EC, KEGG Pathway (MAP00230); BRENDA (EC • Structure: PDB (1AK5), SCOP (, CATH (1AK5) • Family: Pfam (PF00478), BLOCKS (BL00487), PROSITE (PS00487)

  3. PIR Web Site (http://pir.georgetown.edu)

  4. Text Search Result with NULL/NOT NULL

  5. Peptide Search Results

  6. Test Sequence: ftp://nbrfa.georgetown.edu/pir/misc/test.seq PIR-NREF Search Result (I)

  7. PIR-NREF Search Result (II)

  8. PIR Pattern Search

  9. PIR Pattern Search Result (I) Pattern Match: Sequence vs. PROSITE • http://pir.georgetown.edu/pirwww/search/patmatch.html

  10. Search a query pattern against a sequence database. PIR Pattern Search Result (II)

  11. PIR Domain Display

  12. PIR-NREF Database (http://pir.georgetown.edu/pirwww/search/pirnref.shtml) . search

  13. PIR-NREF Report

  14. PIR-iProClass Database

  15. iProClass Sequence Report

  16. PDB Structure of Molecule: Inosine-5'-Monophosphate Dehydrogenase

  17. Related Sequences

  18. Protein Family Classification Discovery of New Knowledge by Using Information Embedded within Families of Homologous Sequences and Their Structures • Superfamily, Domain, and Motif Classification • Superfamily Concept • End-to-End Similarity & Same Overall Domain Architecture • Significance • Improve Sensitivity of Protein Identification • Provide Complete Clustering for Database Organization • Detect and Correct Genome Annotation Errors Systematically • Drive Other Annotations • Stimulate Evolution, Genomics and Proteomics Research

  19. Protein Family/Superfamily Definitions • Family • A Set of Protein Sequences That Share a Common Evolutionary Ancestor with End-to-End Sequence Similarity (No Major Discrepancy by Standard Multiple Alignment Methods) • Have the Same Domain Architecture (Except Incomplete or Alternately Spliced) • Overall Sequence Identity >=45% • Superfamily • A Set of Protein Families That Share a Common Evolutionary Ancestor From End-to-end • Have the Same Domain Architecture • Overall Sequence Identity >=20%

  20. Protein Domain Definition • Homology Domain • A Recognizable Region of Similarity • Have a Common Ancestry • Found in Diverse Protein Sequences (in >= 2 Superfamilies) • A Sequence Can Belong to Only One Protein Family and Superfamily, but May Contain More Than One Domains.

  21. Superfamily-Domain-Motif Relationship

  22. Superfamily-Domain Relationship: ~6000 SFs have >=1 Domains • Superfamily for Domain Architecture iProClass Superfamily List • All Superfamilies Containing PF00001

  23. iProClass Superfamily Report

  24. Alignment and Tree View

  25. PIR-Protein Sequence Database

  26. PIR-PSD Entry

  27. BLAST/FASTA Search

  28. PIR FASTA Search Result

  29. Multiple Alignment & Tree View BLAST Search PIR Searches and Aligment

  30. PIR Hidden Markov Model • http://pir.georgetown.edu/pirwww/search/pirhmm.html • HMM Model Building & Sequence Search • One Protein Against All HMMs • All Proteins Against One HMM

  31. Bibliography Submission • View Bibliography Information • View Protein Entry • Submit Citation with Optional Categorization S1

  32. Bibliography Information Display (I) • From PIR-NREF • From Other Curated Database (e.g., SGD)

  33. Bibliography Information Display (II) • From User Submission • From Computer-Mapping (e.g. Gene Symbol)

  34. Oracle Demo • Java Web Interface for Oracle Database Search: (http://pir.georgetown.edu/iproclass.html) • WebDB Interface to Oracle (WebDB) • Tables/Views/Objects • Functions/Procedures/Packages

  35. Proteomic Bioinformatics • Large-Scale Analysis of Proteomic Data: Homology Search for Pathways

More Related