NCBI FieldGuide NCBI Molecular Biology Resources March 2007 Using Entrez

NCBI FieldGuide WWW Access Entrez & BLAST

NCBI FieldGuide Genomes Taxonomy Entrez: Database Integration PubMed abstracts Nucleotide sequences Protein sequences 3-D Structure Word weight VAST BLAST Phylogeny Hard Link Neighbors Related Sequences Neighbors Related Sequences BLink Domains Neighbors Related Structures

NCBI FieldGuide Database Searching with Entrez uUsing limits and field restriction to find human MutL homolog uLinking and neighboring with MutL uMapping SNPs onto structure and the genome

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

NCBI FieldGuide Advanced Search Options Tabs

NCBI FieldGuide More Precise Nucleotides Search nonpolyposis[All Fields] AND colon cancer[Title] AND human[Organism] AND biomol_mrna[Properties] AND srcdb_refseq[Properties] 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 Molecule type biomol_mrna biomol_genomic GenBank division gbdiv_est gbdiv_htg gbdiv_xxx Gene location gene_in_mitochondrion gene_in_chloroplast gene_in_genomic Source Database srcdb_refseq srcdb_pdb srcdb_swiss_prot

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

NCBI FieldGuide Sequence Links Finding Homologs and Structures

NCBI FieldGuide Protein Link BLAST Link Conserved Domains

NCBI FieldGuide Related Proteins: Homologs and Redundancy Redundant Sequences Bacterial Homologs

NCBI FieldGuide BLink: BLAST Link top 200 only Redundant GIs

NCBI FieldGuide BLink: non-redundant relatives zebrafish homolog BLAST

NCBI FieldGuide Related Proteins: Structure Links

NCBI FieldGuide Structures

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

NCBI FieldGuide Mapping Polymorphisms onto Structure

NCBI FieldGuide Entrez SNP "coding nonsynon"[Function Class]

NCBI FieldGuide GeneView: Variations Human MLH1 ATPase domain

NCBI FieldGuide Related Structures

NCBI FieldGuide Mapping Variation Onto Structure Conserved Asn Asn Ile Ile – Val

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

NCBI FieldGuide Maps and Options

NCBI FieldGuide Mapped Variations

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 Amouse B chick B frog B paralogs orthologs gene duplication Completely Annotated Eukaryotic Genomes Homologous UniGene determined for other organisms Protein similarities first Guided by taxonomic tree Includes orthologs and paralogs 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

NCBI FieldGuide The Gene Database Gene Centered Information Unifies LocusLink and microbial Genomes 2.4 million records for 3,822 taxa Human38,603Sea Urchin 30,603 Chimpanzee31,502Mosquito 13,763 Mouse60,746Fruit Fly 21,116 Rat38,117C. elegans 20,935 Dog20,154Fungi168,802 Cow23, 677Green Plants 76,847 Chicken18, 469Archea74,627 Zebrafish38, 594Bacteria1,361,390

NCBI FieldGuide Genes MLH1: One Stop Shopping

NCBI FieldGuide Genes MLH1: One Stop Shopping (cont.)

NCBI FieldGuide Genes: Display Options and Links