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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