1 Global Entrez Search Results Global NCBI (Entrez) Search NCBI - - PDF document

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NCBI FieldGuide

NCBI Molecular Biology Resources

March 2007

Using Entrez

NCBI FieldGuide

WWW Access

Entrez & BLAST

NCBI FieldGuide

Genomes Taxonomy

Entrez: Entrez: Database I

Database Inte tegrat gratio ion

PubMed abstracts Nucleotide sequences Protein sequences

3-D Structure

3 -D Structure

Word weight VAST BLAST BLAST Phylogeny

Hard Link Neighbors Related Sequences Neighbors Related Sequences BLink Domains Neighbors Related Structures

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 and the genome

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NCBI FieldGuide

Global NCBI (Entrez) Search

Human hereditary nonpolyposis colon cancer

NCBI FieldGuide

Global Entrez Search Results

NCBI FieldGuide

Nucleotide Sequences

Nucleotide database now three parts

• EST expressed sequence tags
• GSS genome survey sequences
• CoreNucleotide everything else

NCBI FieldGuide

Advanced Search Options

Tabs

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NCBI FieldGuide

More Precise Nucleotides Search

nonpolyposis[All Fields] AND colon cancer[Title] AND human[Organism] AND biomol_mrna[Properties] AND srcdb_refseq[Properties]

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]

NCBI FieldGuide

Organism Field: NCBI’s Taxonomy

NCBI FieldGuide

Useful Properties Field Terms

Source Database srcdb_refseq srcdb_pdb srcdb_swiss_prot Gene location gene_in_mitochondrion gene_in_chloroplast gene_in_genomic GenBank division gbdiv_est gbdiv_htg gbdiv_xxx Molecule type biomol_mrna biomol_genomic

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NCBI FieldGuide

Human MutL RefSeq

GenBank Records

NCBI FieldGuide

NM_000249: Links

NCBI FieldGuide

Literature Links

OMIM

NCBI FieldGuide

OMIM: Human Disease Genes

Conserved Domain

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NCBI FieldGuide

Sequence Links

Finding Homologs and Structures

NCBI FieldGuide

Protein Link

BLAST Link Conserved Domains

NCBI FieldGuide

BLink: BLAST Link

top 200 only Redundant GIs

NCBI FieldGuide

BLink: non-redundant relatives

zebrafish homolog BLAST

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NCBI FieldGuide

Short Cut: Related Structures

NCBI FieldGuide

• E. coli MutL Structure

Cn3D viewer Conserved Domains 3D Domain Neighbors Structure Neighbors Pubchem compound

NCBI FieldGuide

MLH1 Domain Structure: CDD

ATPase Domain Mismatch Repair Domain

NCBI FieldGuide

MLH1: ATPase Domain

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NCBI FieldGuide

Mapping Polymorphisms onto Structure

NCBI FieldGuide

GeneView: Variations Human MLH1

ATPase domain

NCBI FieldGuide

Related Structures

NCBI FieldGuide

Mapping Variation Onto Structure

Conserved Asn Asn Ile Ile – Val

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NCBI FieldGuide

Genome Resources

NCBI FieldGuide

NM_000249: Genome Links

NCBI FieldGuide

The Map Viewer

Genome BLAST

NCBI FieldGuide

Map Viewer: Human MLH1

Customizable

NCBI Assembly EST Hits Gene Annotations Models Transcripts

Download data and sequences

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NCBI FieldGuide

Synteny: Mammalian Genomes

Albumin Gene Family

NCBI FieldGuide

Homologene

early globin gene A-chain gene B-chain gene frog A chick A mouse A mouse B chick B frog B paralogs

• rthologs orthologs

gene duplication

• Completely Annotated Eukaryotic

Genomes

• Homologous UniGene

determined for other organisms

• Protein similarities first
• Guided by taxonomic tree
• Includes orthologs and paralogs

NCBI FieldGuide

Homologene Cluster

NCBI FieldGuide

Rice Homolog

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NCBI FieldGuide

The Gene Database

• Gene Centered Information
• Unifies LocusLink and microbial Genomes
• 2.4 million records for 3,822 taxa

74,627 Archea 18, 469 Chicken 76,847 Green Plants 23, 677 Cow 20,935

• C. elegans

38,117 Rat 1,361,390 Bacteria 38, 594 Zebrafish 168,802 Fungi 20,154 Dog 21,116 Fruit Fly 60,746 Mouse 13,763 Mosquito 31,502 Chimpanzee 30,603 Sea Urchin 38,603 Human

NCBI FieldGuide

Genes MLH1: One Stop Shopping

NCBI FieldGuide

Genes MLH1: One Stop Shopping (cont.)

NCBI FieldGuide

Genes: Display Options and Links