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Biological databases

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Biological databases

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Biological databases

  1. 1. Databases
  2. 2. INSDC International Nucleotide Sequence Database Collaboration GenBank EMBL DDBJ Sequence types: Eukaryotic gene Bacterial operon Artificial Cloning vectors Plasmid Repeat element Transfer RNA
  3. 3. GenBank Nucleic Acids Research, 2008, 36, D25-D30
  4. 4. GenBank Doubled in size about every 18 months 80 billion nucleotide bases from more than 76 million individual sequences
  5. 5. Sequence-based taxonomy
  6. 6. 2,60,000 named species 1700 species are being added per month 12 % are human origin & 8% are human EST The top species Homo sapiens ------- 12.7 billion Mus musculus ------- 8.3 billion Rattus norvegicus ------- 5.8 billion Bos taurus ------- 3.8 billion Zea mays ------- 3.6 billion
  7. 7. GenBank Records and Divisions
  8. 8. GenBank records Partitioned into “divisions” Traditional BCT, VRL, PRI, ROD Recent EST, GSS, HTG, HTC, ENV WGS Special TPA
  9. 9. WGS Accession numbers are issued to these sequences eg., AAAA01072744 AAAA Project ID 01 Version number 072744 Contig number TPA Third party annotation 1. Experimental 2. Inferential
  10. 10. Data submission
  11. 11. BankIt Use BankIt if: you have one or a few sequence submissions you prefer to use a WWW-based submission tool your sequence annotation is not complicated you do not require sequence analysis tools to submit your sequence(s)
  12. 12. Sequin Use Sequin if: you are submitting long or complex submissions you are submitting mutation, phylogenetic, population, environmental, or segmented sets you would like graphical viewing and editing options, including the alignment editor you would like network access to related analytical tools
  13. 13. EMBL
  14. 14. EMBL Maintained by EBI Other databases of EBI Swiss-Prot TrEMBL UniProt InterPro E-MSD ArrayExpress
  15. 15. EMBL Taxonomic Invertebrates, Organells, Bacteriophages, Plants, Prokaryotes, Rodents Non-Taxonomic HTG, HTC, GSS, WGS, EST
  16. 16. EMBL representation For Genomic data Coding strand cDNA data RNA sequence tRNA Mature transcript WebIn Data submission tool
  17. 17. DDBJ
  18. 18. DDBJ Entry, format, abbreviation key same as GenBank SAKURA Data submission tool
  19. 19. Secondary Nucleotide Sequence Databases
  20. 20. UniGene Database of unique gene clusters
  21. 21. STACK (Sequence Tag Alignment and Consensus Knowledgebase) Ribosomal database HIV sequence database EPD (Eukaryotic Promoter Database) REBASE
  22. 22. SwissProt Curated protein sequence database High level of annotation Description of the function Domains structure PTMs Variants TrEMBL Consists of entries in SWISS-PROT-like format
  23. 23. PIR-PSD Protein Information resource- Protein Sequence Database World’s first database of classified and funtionally annotated protein sequences Grew out of The Atlas of Protein Sequence and Structure
  24. 24. UniProt Universal Protein Resource Comprehensive resource for protein sequence and annotated data
  25. 25. Sequence Alignments Alignments: Pairwise Multiple Multiple Sequence Alignments provide information on, Alignment itself Consensus Sequences Conserved residues Conserved residue patterns Sequence Profiles
  26. 26. Consensus Sequence Databases Multiple Alignment ↓ A single sequence in which each residue is the most common or consensus for the sequence family ↓ Consensus Sequence Database
  27. 27. Consensus Sequence Databases  Disadvantage: Much information from the sequences that do not contain the consensus residue is ignored, even though these hold information about allowed substitutions.
  28. 28. PROSITE  Database of sequence patterns  Associated with protein family membership.  Developed using patterns that best fit particular protein families and functions.
  29. 29. PROSITE Serine Protease Family :-  Pattern1: [LIVM]-[ST]-A-[STAG]-H-C  Pattern2: [DNSTAGC]-[GSTAPIMVQH]-x(2)-G-[DE]-S-G-[GS]-[SAPHV]- [LIVMFYWH]-PA-[LIVMFYSTANQH]
  30. 30. PROSITE Features: 1.Much shorter than total sequence length 2.Provide information on acceptable substitution. 3.Provide information on shared biological functions.
  31. 31. PROSITE Disadvantage: 1. Lack of specificity. 2. They have no way of attaching probabilities to the variation.
  32. 32. PRINTS and BLOCKS  Contain multiply aligned ungapped segments. BLOCKS- blocks PRINTS - motifs
  33. 33. PRINTS and BLOCKS  Advantages 1. Potentially more sensitive (more distant relationships can be found) 2.More specific (fewer false positives occur)
  34. 34. Specialized Sequence Database  rRNA database  tRNA database  5S rRNA database  Promoter sequence database  InBase, a database on inteins
  35. 35. OMIM  Online Mendelian Inheritance in Man  Comprehensive database of human genes and genetic disorders.  Has numerous links to databases like SWISS- PROT, PubMed, Mutation databases, Mapviewer.
  36. 36. Structural Databases  RCSB 1. PDB 2. NDB
  37. 37. Structural Databases  PDBe of EBI  MMDB Structures derived from the PDB, with value-added features such as, Explicit chemical graphs, Links to literature, Similar sequences, Related 3D structures, Information about chemicals
  38. 38. Structural Databases CATH C- Class A- Architecture T- Topology H- Homologous superfamily SCOP Structural Classification of Proteins
  39. 39. Higher Order Functions Databases  KEGG (Kyoto Encyclopedia of Genes and Genomes) Subsidiary Databases Contains 16 main databases
  40. 40. Higher Order Functions Databases  DIP (Database of Interacting Proteins)  BIND (Biomolecular Interaction Network Database)
  41. 41. Literature Databases  PubMed  Web of Science  BioMedNet
  42. 42. Data retrieval tools
  43. 43. Data retrieval tools Entrez

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