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NCBI FieldGuide NCBI Molecular Biology Resources January 2008 Using Entrez.

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Presentation on theme: "NCBI FieldGuide NCBI Molecular Biology Resources January 2008 Using Entrez."— Presentation transcript:

1 NCBI FieldGuide NCBI Molecular Biology Resources January 2008 Using Entrez

2 NCBI FieldGuide WWW Access Entrez & BLAST

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

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

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

6 NCBI FieldGuide The Links Menu: Access to Neighbors and Links Neighbors Hard Links

7 NCBI FieldGuide Database Searching with Entrez uUsing limits and field restriction to find human MutL homolog uLinking and neighboring with MutL uMapping SNPs onto structure

8 NCBI FieldGuide Global NCBI (Entrez) Search colon cancer

9 NCBI FieldGuide Global Entrez Search Results

10 NCBI FieldGuide OMIM: Human Disease Genes Conserved Domain

11 NCBI FieldGuide Nucleotide Sequences Nucleotide database now three parts EST expressed sequence tags GSS genome survey sequences CoreNucleotide everything else

12 NCBI FieldGuide Core Nucleotide Results with Gene Preview New! Gene Preview more relevant results New! Gene Preview more relevant results New! Taxonomy Filters

13 NCBI FieldGuide Advanced Search Options Tabs Taxonomy filter

14 NCBI FieldGuide More Precise Nucleotides Search colon cancer[Title] AND nonpolyposis[Title] AND human[Organism] AND biomol_mrna[Properties] AND srcdb_refseq[Properties]

15 NCBI FieldGuide 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]

16 NCBI FieldGuide Entrez Tip: Start Searches in Gene UniGen e Other Entrez DBs BLink Homologene: Gene Neighbors

17 NCBI FieldGuide Gene Results nonpolyposis colon cancer AND human[Organism]

18 NCBI FieldGuide Precise Results MLH1[Gene Name] AND Human[Organism] NCBI Taxonomy

19 NCBI FieldGuide Organism Field: NCBI’s Taxonomy All molecular databases All molecular databases

20 NCBI FieldGuide MLH1 Gene Record

21 NCBI FieldGuide MLH1 Gene Record: Interactions and GO

22 NCBI FieldGuide MLH1 Sequences

23 NCBI FieldGuide MLH1 Gene Record: Sequences

24 NCBI FieldGuide MLH1: Sequence Links

25 NCBI FieldGuide Gene Table: Genomic Sequences

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

27 NCBI FieldGuide MLH1 Homologs

28 NCBI FieldGuide Synteny: Mammalian Genomes Albumin Gene Family

29 NCBI FieldGuide Finding Homologs: HomoloGene Gene

30 HomoloGene Cluster Gene Links Protein Links

31 HomoloGene Downloader Protien mRNA Genomic Protien mRNA Genomic

32 NCBI FieldGuide Finding Homologs 2: BLink Gene Protein

33 NCBI FieldGuide BLink: BLAST Link (Best Hits) Redundant Proteins First 200 only BLAST Tomato homolog

34 NCBI FieldGuide Finding Polymorphisms Gene

35 NCBI FieldGuide GeneView: Variations Human MLH1 ATPase domain

36 NCBI FieldGuide MLH1 Structure Model and Mapping Polymorphisms

37 NCBI FieldGuide Related Structures: structure model

38 NCBI FieldGuide Sequence Similar Structures Conserved Domain Conserved Domain Link to Structure Link to Alignment

39 NCBI FieldGuide E. coli MutL Structure Cn3D viewer Conserved Domains

40 NCBI FieldGuide Alignment Based Model : Mapping Polymorphisms Mg 2+ binding site Ile - Val

41 NCBI FieldGuide Better Model: Conserved Domain Gene Protein Related Structures

42 NCBI FieldGuide Better Model: Conserved Domain Mg 2+ binding site Ile – Val Position 32 Ile – Val Position 32


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