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Archives and Information Retrieval Lecture by; AQSAD  RASHDA BIOINFORMATICS
Database indexing and specification of search terms ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Primary data collections related to biological macromolecules include: 􀂃  Nucleic acid sequences, including whole-genome projects 􀂃  Amino acid sequences of proteins 􀂃  Protein and nucleic acid structures 􀂃  Small-molecule crystal structures 􀂃  Protein functions 􀂃  Expression patterns of genes 􀂃  Publications The archives
Nucleic acid sequence databases ,[object Object],[object Object],[object Object],[object Object],[object Object]
Nucleotide sequence databases  ,[object Object],[object Object],[object Object],[object Object]
 
 
The EMBL data library entry for the bovine pancreatic trypsin inhibitor gene Organism Classification Keyword Description Date Identification Accession Organism Source Reference Number
Reference Title Reference Author Reference Position Reference Location Feature Table Header
FT:  The feature table may indicate regions that 1. perform or affect function 2.  interact with other molecules 3.  affect replication 4. are involved in recombination 5. are a repeated unit 6. have secondary or tertiary structure 7. are revised or corrected Sequence Header
Protein sequence databases ,[object Object],[object Object]
http://pir.georgetown.edu/
PIR entry for the amino acid sequence of Bovine pancreatic trypsin inhibitor
 
 
Databases associated with SWISS-PROT ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
A Sample Entry in ENZYME DB
The PIR and associated databases ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Databases of structures ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
 
Protein data bank entry 2TRX,  E. coli  thioredoxin
 
 
 
 
 
Indicators of structure quality ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Classifications of protein structures ,[object Object],[object Object],[object Object],[object Object]
Specialized, or 'boutique' databases ,[object Object],[object Object],[object Object],[object Object],[object Object]
Web Resource: Databases for Specific Protein Families ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Expression and proteomics databases ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
To be Continued………..

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Databases

  • 1. Archives and Information Retrieval Lecture by; AQSAD RASHDA BIOINFORMATICS
  • 2.
  • 3. Primary data collections related to biological macromolecules include: 􀂃 Nucleic acid sequences, including whole-genome projects 􀂃 Amino acid sequences of proteins 􀂃 Protein and nucleic acid structures 􀂃 Small-molecule crystal structures 􀂃 Protein functions 􀂃 Expression patterns of genes 􀂃 Publications The archives
  • 4.
  • 5.
  • 6.  
  • 7.  
  • 8. The EMBL data library entry for the bovine pancreatic trypsin inhibitor gene Organism Classification Keyword Description Date Identification Accession Organism Source Reference Number
  • 9. Reference Title Reference Author Reference Position Reference Location Feature Table Header
  • 10. FT: The feature table may indicate regions that 1. perform or affect function 2. interact with other molecules 3. affect replication 4. are involved in recombination 5. are a repeated unit 6. have secondary or tertiary structure 7. are revised or corrected Sequence Header
  • 11.
  • 13. PIR entry for the amino acid sequence of Bovine pancreatic trypsin inhibitor
  • 14.  
  • 15.  
  • 16.
  • 17. A Sample Entry in ENZYME DB
  • 18.
  • 19.
  • 20.  
  • 21. Protein data bank entry 2TRX, E. coli thioredoxin
  • 22.  
  • 23.  
  • 24.  
  • 25.  
  • 26.  
  • 27.
  • 28.
  • 29.
  • 30.
  • 31.