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					                                    NCBI FieldGuide
           NCBI Molecular Biology
                 Resources

                Using Entrez




January 2008
         NCBI FieldGuide
WWW
Access

Entrez
&
BLAST
     Entrez: Database Integration




                                                                        NCBI FieldGuide
                                      Word weight

                          PubMed
                          abstracts



        Homologene                              3 -D
                                                3-D
                                             Structure
                                             Structure
                                                                VAST
                           Gene
                                                         Neighbors
                                                         Related Structures


             Nucleotide                   Protein
BLAST                                                    BLAST
             sequences                  sequences
                                                     Neighbors
Neighbors
                            Hard Link                Related Sequences
Related Sequences
                                                     BLink
                                                     Domains
The Links Menu:   Access to Neighbors and Links




                                                  NCBI FieldGuide
                                   SNP



           GEO


                                   Gene

                     PubMed




                                          Protein
The Links Menu:   Access to Neighbors and Links




                                                  NCBI FieldGuide
                  Neighbors: BLAST Link
                  pre-computed BLAST




            Neighbors:
            pre-computed CDD search
The Links Menu:    Access to Neighbors and Links




                                                   NCBI FieldGuide
       Neighbors




                                         Hard Links
                                                                 NCBI FieldGuide
Database Searching with Entrez
Using limits and field restriction to find human MutL homolog
Linking and neighboring with MutL
Mapping SNPs onto structure
       Global NCBI (Entrez) Search




                                     NCBI FieldGuide
colon cancer
Global Entrez Search Results




                               NCBI FieldGuide
 Nucleotide Sequences




                                       NCBI FieldGuide
 Nucleotide database now three parts

•EST expressed sequence tags
•GSS genome survey sequences
•CoreNucleotide everything else
Core Nucleotide Results with Gene Preview




                                            NCBI FieldGuide
    New! Gene Preview
    more relevant results




              New! Taxonomy Filters
Advanced Search Options




                                       NCBI FieldGuide
              Tabs




                     Taxonomy filter
  More Precise Nucleotides Search




                                                                  NCBI FieldGuide
colon cancer[Title] AND nonpolyposis[Title] AND human[Organism]
AND biomol_mrna[Properties] AND srcdb_refseq[Properties]
                Useful Field Restrictions




                                                                                 NCBI FieldGuide
[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]
        Entrez Tip: Start Searches in Gene




                                                  NCBI FieldGuide
                                 BLink




Other Entrez DBs


                                 Homologene:
                                 Gene Neighbors
       Gene Results




                                                NCBI FieldGuide
nonpolyposis colon cancer AND human[Organism]
   Precise Results




                                        NCBI FieldGuide
MLH1[Gene Name] AND Human[Organism]



                        NCBI Taxonomy
Organism Field: NCBI’s Taxonomy




                                  NCBI FieldGuide
             All molecular
             databases
MLH1 Gene Record




                   NCBI FieldGuide
MLH1 Gene Record: Interactions and GO




                                        NCBI FieldGuide
NCBI FieldGuide
                  MLH1 Sequences
MLH1 Gene Record: Sequences




                              NCBI FieldGuide
MLH1: Sequence Links




                       NCBI FieldGuide
Gene Table: Genomic Sequences




                                NCBI FieldGuide
  Map Viewer: All Sequences




                                                             NCBI FieldGuide
                           Customizable



                            Transcripts
                EST Hits


                    Download data and sequences


           Models


NCBI Assembly


                                          Gene Annotations
NCBI FieldGuide
                  MLH1 Homologs
Synteny: Mammalian Genomes




                                      NCBI FieldGuide
                Albumin Gene Family
Finding Homologs: HomoloGene




                               NCBI FieldGuide
 Gene
                   HomoloGene
                       Cluster




Gene Links
             Protein Links
           HomoloGene
            Downloader
 Protien
 mRNA
Genomic
   Finding Homologs 2: BLink




                                   NCBI FieldGuide
Gene




                         Protein
BLink: BLAST Link (Best Hits)




                                           NCBI FieldGuide
                      Redundant Proteins


                         First 200 only




                     Tomato homolog




      BLAST
 Finding Polymorphisms




                         NCBI FieldGuide
Gene
GeneView: Variations Human MLH1




                                     NCBI FieldGuide
                          ATPase domain
                           NCBI FieldGuide
MLH1 Structure Model and
 Mapping Polymorphisms
Related Structures: structure model




                                      NCBI FieldGuide
Sequence Similar Structures




                                                 NCBI FieldGuide
                                     Conserved
                                      Domain




   Link to Structure
                       Link to Alignment
E. coli MutL Structure




                                NCBI FieldGuide
              Cn3D viewer




            Conserved Domains
Alignment Based Model: Mapping Polymorphisms




                                               NCBI FieldGuide
                     Mg2+ binding site




             Ile - Val
Better Model: Conserved Domain




                                               NCBI FieldGuide
Gene




                Protein




                          Related Structures
Better Model: Conserved Domain




                                     NCBI FieldGuide
                 Mg2+ binding site




   Ile – Val
   Position 32

				
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posted:7/27/2011
language:English
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