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NCBI Molecular Biology Resources

NCBI Molecular Biology Resources. Using Entrez. January 2008. WWW Access. Entrez & BLAST. Entrez: Database Integration. Word weight. PubMed abstracts. 3-D Structure. 3 -D Structure. Homologene. VAST. Gene. Neighbors Related Structures. Protein sequences. Nucleotide sequences.

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NCBI Molecular Biology Resources

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  1. NCBI Molecular Biology Resources Using Entrez January 2008

  2. WWWAccess Entrez & BLAST

  3. Entrez: Database Integration Word weight PubMed abstracts 3-D Structure 3 -D Structure Homologene VAST Gene Neighbors Related Structures Protein sequences Nucleotide sequences BLAST BLAST Neighbors Related Sequences BLink Domains Neighbors Related Sequences Hard Link

  4. SNP GEO Gene PubMed Protein The Links Menu: Access to Neighbors and Links

  5. Neighbors: BLAST Link pre-computed BLAST Neighbors: pre-computed CDD search The Links Menu: Access to Neighbors and Links

  6. Neighbors Hard Links The Links Menu: Access to Neighbors and Links

  7. Database Searching with Entrez Using limits and field restriction to find human MutL homolog Linking and neighboring with MutL Mapping SNPs onto structure

  8. colon cancer Global NCBI (Entrez) Search

  9. Global Entrez Search Results

  10. Nucleotide Sequences • Nucleotide database now three parts • EST expressed sequence tags • GSS genome survey sequences • CoreNucleotide everything else

  11. New! Gene Preview more relevant results New! Taxonomy Filters Core Nucleotide Results with Gene Preview

  12. Advanced Search Options Tabs Tabs Taxonomy filter

  13. More Precise Nucleotides Search colon cancer[Title] AND nonpolyposis[Title] AND human[Organism] AND biomol_mrna[Properties] AND srcdb_refseq[Properties]

  14. Useful Field Restrictions • [Title]: Definition line in GenBank / GenPept format shown in Summary format • glyceraldehyde 3 phosphate dehydrogenase[Title] • [Organism]: NCBI’s taxonomy. Organizing system for molecular databases • mouse[organism]; green plants[organism]; Streptomyces coelicolor[organism] • [Properties]: molecule type, location, database source • biomol_mrna[properties]; biomol_genomic[properties]; • gene_in_mitochondrion[properties];srcdb pdb[properties] • [Filter]: subsets of data, Entrez links • all[filter]; nucleotide mapview[filter]; nucleotide omim[filter]

  15. Entrez Tip: Start Searches in Gene BLink Homologene: Gene Neighbors

  16. Gene Results nonpolyposis colon cancer AND human[Organism]

  17. Precise Results MLH1[Gene Name] AND Human[Organism] NCBI Taxonomy

  18. Organism Field: NCBI’s Taxonomy All molecular databases

  19. MLH1 Gene Record

  20. MLH1 Gene Record: Interactions and GO

  21. MLH1 Sequences

  22. MLH1 Gene Record: Sequences

  23. MLH1: Sequence Links

  24. Gene Table: Genomic Sequences

  25. Map Viewer: All Sequences Customizable Transcripts EST Hits Download data and sequences Models NCBI Assembly Gene Annotations

  26. MLH1 Homologs

  27. Synteny: Mammalian Genomes Albumin Gene Family

  28. Finding Homologs: HomoloGene Gene

  29. Gene Links Protein Links HomoloGene Cluster

  30. HomoloGene Downloader Protien mRNA Genomic

  31. Finding Homologs 2: BLink Gene Protein

  32. BLink: BLAST Link (Best Hits) Redundant Proteins First 200 only Tomato homolog BLAST

  33. Finding Polymorphisms Gene

  34. ATPase domain GeneView: Variations Human MLH1

  35. MLH1 Structure Model and Mapping Polymorphisms

  36. Related Structures: structure model

  37. Sequence Similar Structures Conserved Domain Link to Structure Link to Alignment

  38. E. coli MutL Structure Cn3D viewer Conserved Domains

  39. Alignment Based Model: Mapping Polymorphisms Mg2+ binding site Ile - Val

  40. Better Model: Conserved Domain Gene Protein Related Structures

  41. Better Model: Conserved Domain Mg2+ binding site Ile – Val Position 32

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