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COT 6930 HPC and Bioinformatics Bioinformatics Resources and Databases sree
DNA RNA cDNA ESTs UniGene phenotype Genomic DNA Databases Protein sequence databases protein Protein structure databases transcription translation Gene expression database
Gene
Different transcripts can be related to the same gene !
EST ,[object Object],[object Object],[object Object]
Outline ,[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]
Bioinformatics Databases ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Primary public domain bioinformatics servers Public Domain Bioinformatics Facilities European Bioinformatics Institute (EBI) United Kingdom National Center For Biotechnology Information (NCBI) United States Genome Net (KEGG & DDBJ) Japan Databases Analysis Tools Databases Analysis Tools Databases Analysis Tools
Major Databases ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Bioinformatics Data Sources ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Bioinformatics Data Sources ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Outline ,[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]
Bioinformatic Databases – GenBank ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Bioinformatic Databases – GenBank ,[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]
Bioinformatic Databases – EMBL-Bank ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Outline ,[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]
Bioinformatic Databases – Proteins ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Bioinformatic Databases – Swiss-Prot, PIR-PSD ,[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]
Bioinformatic Databases – GenPept, TrEMBL ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Structure Databases ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Protein Data Bank: PDB
 
Bioinformatic Databases – Connections
Outline ,[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]
Bioinformatic Databases – RefSeq ,[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]
Bioinformatic Databases – UniGene ,[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],[object Object],[object Object],[object Object],Bioinformatic Databases – PubMed
Bioinformatic Databases – Others ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Bioinformatic Databases: SNP Database ,[object Object],[object Object],[object Object],[object Object]
Sickle Cell Anemia ,[object Object],Image source: http://www.cc.nih.gov/ccc/ccnews/nov99/
Healthy Individual ,[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]
Diseased Individual ,[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]
Disease Databases ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
 
Putting it All Together ,[object Object],[object Object]
GENOMIC DATA GenBank DDBJ EMBL ASSEMBLED GENOMES GoldenPath WormBase TIGR PROTEIN PIR SWISS-PROT STRUCTURE PDB MMDB SCOP LITERATURE PubMed PATHWAY KEGG COG DISEASE LocusLink OMIM OMIA GENES RefSeq AllGenes GDB SNPs dbSNP ESTs dbEST unigene MOTIFS BLOCKS Pfam Prosite GENE EXPRESSION Stanford MGDB NetAffx ArrayExpress
Where to get started? NCBI ENTREZ ,[object Object],ENTREZ PubMed GenBank Protein databases Genomes SNP Taxonomy OMIM http://www.ncbi.nlm.nih.gov/sites/gquery
Outline ,[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]

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Biodatabases 101220022654-phpapp02

  • 1. COT 6930 HPC and Bioinformatics Bioinformatics Resources and Databases sree
  • 2. DNA RNA cDNA ESTs UniGene phenotype Genomic DNA Databases Protein sequence databases protein Protein structure databases transcription translation Gene expression database
  • 4. Different transcripts can be related to the same gene !
  • 5.
  • 6.
  • 7.
  • 8. Primary public domain bioinformatics servers Public Domain Bioinformatics Facilities European Bioinformatics Institute (EBI) United Kingdom National Center For Biotechnology Information (NCBI) United States Genome Net (KEGG & DDBJ) Japan Databases Analysis Tools Databases Analysis Tools Databases Analysis Tools
  • 9.
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  • 15.
  • 16.
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  • 18.
  • 19.
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  • 25.
  • 26.
  • 27.
  • 28.
  • 29.
  • 30.
  • 31.
  • 32.
  • 33.
  • 34.  
  • 35.
  • 36. GENOMIC DATA GenBank DDBJ EMBL ASSEMBLED GENOMES GoldenPath WormBase TIGR PROTEIN PIR SWISS-PROT STRUCTURE PDB MMDB SCOP LITERATURE PubMed PATHWAY KEGG COG DISEASE LocusLink OMIM OMIA GENES RefSeq AllGenes GDB SNPs dbSNP ESTs dbEST unigene MOTIFS BLOCKS Pfam Prosite GENE EXPRESSION Stanford MGDB NetAffx ArrayExpress
  • 37.
  • 38.