NCBI FieldGuide NCBI Molecular Biology Resources March 2007 Using Entrez.
NCBI FieldGuide NCBI Molecular Biology Resources January 2008 Using Entrez.
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Transcript of NCBI FieldGuide NCBI Molecular Biology Resources January 2008 Using Entrez.
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NCBI Molecular Biology Resources
January 2008
Using Entrez
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eWWWAccess
Entrez&BLAST
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Gene
Homologene
Entrez: Database Integration
PubMed abstracts
Nucleotide sequences
Protein sequences
3-D Structure
3 -D Structure
Word weight
VAST
BLASTBLAST
Hard LinkNeighborsRelated Sequences
NeighborsRelated SequencesBLinkDomains
NeighborsRelated Structures
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eThe Links Menu: Access to Neighbors and
LinksSNPSNP
GEOGEO
GeneGene
PubMedPubMed
ProteinProtein
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eThe Links Menu: Access to Neighbors and
LinksNeighbors: BLAST Linkpre-computed BLASTNeighbors: BLAST Linkpre-computed BLAST
Neighbors:pre-computed CDD searchNeighbors:pre-computed CDD search
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eThe Links Menu: Access to Neighbors and
Links
NeighborsNeighbors
Hard LinksHard Links
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Database Searching with Entrez
Using limits and field restriction to find human MutL homologLinking and neighboring with MutLMapping SNPs onto structure
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Global NCBI (Entrez) Search
colon cancercolon cancer
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Global Entrez Search Results
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Nucleotide Sequences
Nucleotide database now three parts
•EST expressed sequence tags•GSS genome survey sequences•CoreNucleotide everything else
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Core Nucleotide Results with Gene Preview
New! Gene Previewmore relevant resultsNew! Gene Previewmore relevant results
New! Taxonomy FiltersNew! Taxonomy Filters
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Advanced Search OptionsTabsTabs
Taxonomy filterTaxonomy filter
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eMore Precise Nucleotides
Search
colon cancer[Title] AND nonpolyposis[Title] AND human[Organism] AND biomol_mrna[Properties] AND srcdb_refseq[Properties]colon cancer[Title] AND nonpolyposis[Title] AND human[Organism] AND biomol_mrna[Properties] AND srcdb_refseq[Properties]
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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]
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eEntrez Tip: Start Searches in
Gene
HomoloGene
Entrez Protein
Gene
UniGene
Other Entrez DBs
BLink
Homologene:Gene Neighbors
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Gene Results nonpolyposis colon cancer AND human[Organism]nonpolyposis colon cancer AND human[Organism]
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Precise Results
MLH1[Gene Name] AND Human[Organism]MLH1[Gene Name] AND Human[Organism]
NCBI TaxonomyNCBI Taxonomy
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Organism Field: NCBI’s Taxonomy
All molecular databasesAll molecular databases
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MLH1 Gene Record
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eMLH1 Gene Record: Interactions and
GO
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MLH1 Sequences
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MLH1 Gene Record: Sequences
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MLH1: Sequence Links
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Gene Table: Genomic Sequences
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Map Viewer: All SequencesCustomizableCustomizable
NCBI Assembly
EST Hits
Gene Annotations
Models
Transcripts
Download data and sequencesDownload data and sequences
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MLH1 Homologs
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eSynteny: Mammalian Genomes
Albumin Gene FamilyAlbumin Gene Family
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Finding Homologs: HomoloGene
GeneGene
HomoloGene Cluster
Gene LinksGene LinksProtein LinksProtein Links
HomoloGene Downloader
ProtienmRNA
Genomic
ProtienmRNA
Genomic
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Finding Homologs 2: BLink
GeneGene
ProteinProtein
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BLink: BLAST Link (Best Hits)
Redundant ProteinsRedundant Proteins
First 200 onlyFirst 200 only
BLASTBLAST
Tomato homologTomato homolog
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Finding Polymorphisms
GeneGene
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eGeneView: Variations Human
MLH1
ATPase domain
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MLH1 Structure Model and Mapping Polymorphisms
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Related Structures: structure model
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Sequence Similar Structures
ConservedDomain
ConservedDomain
Link to StructureLink to StructureLink to AlignmentLink to Alignment
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E. coli MutL Structure
Cn3D viewerCn3D viewer
Conserved DomainsConserved Domains
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Alignment Based Model: Mapping Polymorphisms
Mg2+ binding siteMg2+ binding site
Ile - ValIle - Val
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Better Model: Conserved Domain
GeneGene
ProteinProtein
Related StructuresRelated Structures
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Better Model: Conserved Domain
Mg2+ binding siteMg2+ binding site
Ile – ValPosition 32Ile – ValPosition 32