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NCBI Molecular Biology Resources

NCBI Molecular Biology Resources. Using Entrez. March 2007. WWW Access. Entrez & BLAST. Entrez: Database Integration. Word weight. PubMed abstracts. 3 -D Structure. 3-D Structure. Taxonomy. VAST. Genomes. Phylogeny. Neighbors Related Structures. Protein sequences.

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NCBI Molecular Biology Resources

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  1. NCBI Molecular Biology Resources Using Entrez March 2007

  2. WWWAccess Entrez & BLAST

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

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

  5. Human hereditary nonpolyposis colon cancer Global NCBI (Entrez) Search

  6. Global Entrez Search Results

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

  8. Advanced Search Options Tabs

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

  10. 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]

  11. Organism Field: NCBI’s Taxonomy

  12. Useful Properties Field Terms

  13. GenBank Records Human MutL RefSeq

  14. NM_000249: Links

  15. Literature Links OMIM

  16. Conserved Domain OMIM: Human Disease Genes

  17. Sequence Links Finding Homologs and Structures

  18. Protein Link BLAST Link Conserved Domains

  19. BLink: BLAST Link Redundant GIs top 200 only

  20. BLink: non-redundant relatives zebrafish homolog BLAST

  21. Short Cut: Related Structures

  22. E. coli MutL Structure Cn3D viewer Structure Neighbors 3D Domain Neighbors Pubchem compound Conserved Domains

  23. MLH1 Domain Structure: CDD ATPase Domain Mismatch Repair Domain

  24. MLH1: ATPase Domain

  25. Mapping Polymorphisms onto Structure

  26. ATPase domain GeneView: Variations Human MLH1

  27. Related Structures

  28. Mapping Variation Onto Structure Asn Ile Ile – Val Conserved Asn

  29. Genome Resources

  30. NM_000249: Genome Links

  31. The Map Viewer Genome BLAST

  32. Map Viewer: Human MLH1 Customizable Transcripts EST Hits Download data and sequences Models NCBI Assembly Gene Annotations

  33. Synteny: Mammalian Genomes Albumin Gene Family

  34. orthologs orthologs paralogs frog A chick A mouse A mouseB chick B frog B A-chain gene B-chain gene gene duplication early globin gene Homologene • Completely Annotated Eukaryotic Genomes • Homologous UniGene determined for other organisms • Protein similarities first • Guided by taxonomic tree • Includes orthologs and paralogs

  35. Homologene Cluster

  36. Rice Homolog

  37. The Gene Database • Gene Centered Information • Unifies LocusLink and microbial Genomes • 2.4 million records for 3,822 taxa

  38. Genes MLH1: One Stop Shopping

  39. Genes MLH1: One Stop Shopping (cont.)

  40. Genes: Display Options and Links

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