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

NCBI FieldGuide NCBI FieldGuide WWW Access NCBI Molecular Biology Resources Entrez & Using Entrez BLAST March 2007 Entrez: Database I Entrez: Database Inte tegrat gratio ion NCBI FieldGuide NCBI FieldGuide Word weight PubMed abstracts Database Searching with Entrez 3 -D 3-D Taxonomy VAST Structure Structure � Using limits and field restriction to find human MutL homolog Genomes � Linking and neighboring with MutL Phylogeny Neighbors � Mapping SNPs onto structure and the genome Related Structures Protein Nucleotide BLAST BLAST sequences sequences Neighbors Neighbors Related Sequences Hard Link Related Sequences BLink Domains 1

Global Entrez Search Results Global NCBI (Entrez) Search NCBI FieldGuide NCBI FieldGuide Human hereditary nonpolyposis colon cancer Nucleotide Sequences Advanced Search Options NCBI FieldGuide NCBI FieldGuide Tabs Nucleotide database now three parts •EST expressed sequence tags •GSS genome survey sequences •CoreNucleotide everything else 2

Useful Field Restrictions More Precise Nucleotides Search NCBI FieldGuide 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] nonpolyposis[All Fields] AND colon cancer[Title] AND human[Organism] [Filter]: subsets of data, Entrez links AND biomol_mrna[Properties] AND srcdb_refseq[Properties] all[filter]; nucleotide mapview[filter]; nucleotide omim[filter] Organism Field: NCBI’s Taxonomy Useful Properties Field Terms NCBI FieldGuide NCBI FieldGuide Molecule type GenBank division biomol_mrna gbdiv_est biomol_genomic gbdiv_htg gbdiv_xxx Gene location Source Database gene_in_mitochondrion srcdb_refseq gene_in_chloroplast srcdb_pdb gene_in_genomic srcdb_swiss_prot 3

NM_000249: Links Human MutL RefSeq NCBI FieldGuide NCBI FieldGuide GenBank Records OMIM: Human Disease Genes NCBI FieldGuide NCBI FieldGuide Literature Links OMIM Conserved Domain 4

Protein Link NCBI FieldGuide NCBI FieldGuide BLAST Link Conserved Domains Sequence Links Finding Homologs and Structures BLink: BLAST Link BLink: non-redundant relatives NCBI FieldGuide NCBI FieldGuide Redundant GIs top 200 only zebrafish homolog BLAST 5

Short Cut: Related Structures E. coli MutL Structure NCBI FieldGuide NCBI FieldGuide Cn3D viewer Structure Neighbors 3D Domain Neighbors Pubchem compound Conserved Domains MLH1 Domain Structure: CDD MLH1: ATPase Domain NCBI FieldGuide NCBI FieldGuide ATPase Domain Mismatch Repair Domain 6

GeneView: Variations Human MLH1 NCBI FieldGuide NCBI FieldGuide Mapping Polymorphisms onto Structure ATPase domain Related Structures Mapping Variation Onto Structure NCBI FieldGuide NCBI FieldGuide Asn Ile Ile – Val Conserved Asn 7

NM_000249: Genome Links NCBI FieldGuide NCBI FieldGuide Genome Resources Map Viewer: Human MLH1 The Map Viewer NCBI FieldGuide NCBI FieldGuide Customizable Genome BLAST Transcripts EST Hits Download data and sequences Models NCBI Assembly Gene Annotations 8

Synteny: Mammalian Genomes Homologene NCBI FieldGuide NCBI FieldGuide orthologs orthologs paralogs • Completely Annotated Eukaryotic Genomes frog A chick A mouse A mouse B chick B frog B • Homologous UniGene determined for other organisms • Protein similarities first Albumin Gene Family • Guided by taxonomic tree A-chain gene B-chain gene • Includes orthologs and paralogs gene duplication early globin gene Homologene Cluster Rice Homolog NCBI FieldGuide NCBI FieldGuide 9

The Gene Database Genes MLH1: One Stop Shopping NCBI FieldGuide NCBI FieldGuide • Gene Centered Information • Unifies LocusLink and microbial Genomes • 2.4 million records for 3,822 taxa Human 38,603 Sea Urchin 30,603 Chimpanzee 31,502 Mosquito 13,763 Mouse 60,746 Fruit Fly 21,116 Rat 38,117 C. elegans 20,935 Dog 20,154 Fungi 168,802 Cow 23, 677 Green Plants 76,847 Chicken 18, 469 Archea 74,627 Zebrafish 38, 594 Bacteria 1,361,390 Genes: Display Options and Links Genes MLH1: One Stop Shopping (cont.) NCBI FieldGuide NCBI FieldGuide 10