NCBI Molecular Biology Resources

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Presentation transcript:

NCBI Molecular Biology Resources Using Entrez January 2008

WWW Access Entrez & BLAST

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

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

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

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

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 colon cancer

Global Entrez Search Results

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

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

Advanced Search Options Tabs Tabs Taxonomy filter

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

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]

Entrez Tip: Start Searches in Gene BLink Homologene: Gene Neighbors

Gene Results nonpolyposis colon cancer AND human[Organism]

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

Organism Field: NCBI’s Taxonomy All molecular databases

MLH1 Gene Record

MLH1 Gene Record: Interactions and GO

MLH1 Sequences

MLH1 Gene Record: Sequences

MLH1: Sequence Links

Gene Table: Genomic Sequences

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

MLH1 Homologs

Synteny: Mammalian Genomes Albumin Gene Family

Finding Homologs: HomoloGene

HomoloGene Cluster Gene Links Protein Links

HomoloGene Downloader Protien mRNA Genomic

Finding Homologs 2: BLink Gene Protein

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

Finding Polymorphisms Gene

GeneView: Variations Human MLH1 ATPase domain

MLH1 Structure Model and Mapping Polymorphisms

Related Structures: structure model

Sequence Similar Structures Conserved Domain Link to Structure Link to Alignment

E. coli MutL Structure Cn3D viewer Conserved Domains

Alignment Based Model: Mapping Polymorphisms Mg2+ binding site Ile - Val

Better Model: Conserved Domain Gene Protein Related Structures

Better Model: Conserved Domain Mg2+ binding site Ile – Val Position 32

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