1. NCBI Molecular Biology Resources
Using Entrez
January 2008

2. WWW Access
Entrez
&
BLAST

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

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

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

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

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. Global NCBI (Entrez) Search
colon cancer

9. Global Entrez Search Results

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

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

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

29. HomoloGene Cluster
Gene Links
Protein Links

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. GeneView: Variations Human MLH1
ATPase domain

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