NCBI Molecular Biology Resources. Entrez & BLAST. Entrez: Database Integration. Database Searching with Entrez. WWW Access. Using Entrez.
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1 NCBI Molecular Biology Resources Using Entrez WWW Access Entrez & BLAST March 2007 Phylogeny Entrez: Database Integration Taxonomy PubMed abstracts Genomes Word weight 3-D Structure VAST Neighbors Related Structures 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 BLAST Nucleotide sequences Neighbors Related Sequences Hard Link Protein sequences BLAST Neighbors Related Sequences BLink Domains 1
2 Global NCBI (Entrez) Search Global Entrez Search Results Human hereditary nonpolyposis colon cancer Nucleotide Sequences Advanced Search Options Tabs Nucleotide database now three parts EST expressed sequence tags GSS genome survey sequences CoreNucleotide everything else 2
![More Precise Nucleotides Search Useful Field Restrictions [Title]: Definition line in GenBank / GenPept format shown in](/docs-images/80/81931452/images/3-1.jpg "Summary format glyceraldehyde 3 phosphate dehydrogenase[title] [Organism]: NCBI s taxonomy.")
![Organizing system for molecular databases mouse[organism]; green plants[organism]; Streptomyces coelicolor[organism]](/docs-images/80/81931452/images/3-2.jpg "[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]](/docs-images/80/81931452/images/3-3.jpg "AND biomol_mrna[properties] AND srcdb_refseq[properties] [Filter]: subsets of data, Entrez links all[filter]; nucleotide")
![mapview[filter]; nucleotide omim[filter] Organism Field: NCBI s Taxonomy Useful Properties Field Terms Molecule type](/docs-images/80/81931452/images/3-4.jpg "biomol_mrna biomol_genomic GenBank division gbdiv_est gbdiv_htg gbdiv_xxx Gene location gene_in_mitochondrion")
3 More Precise Nucleotides Search 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] nonpolyposis[all Fields] AND colon cancer[title] AND human[organism] AND biomol_mrna[properties] AND srcdb_refseq[properties] [Filter]: subsets of data, Entrez links all[filter]; nucleotide mapview[filter]; nucleotide omim[filter] Organism Field: NCBI s Taxonomy 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 3
4 Human MutL RefSeq NM_000249: Links GenBank Records OMIM: Human Disease Genes Literature Links OMIM Conserved Domain 4
5 Protein Link BLAST Link Sequence Links Conserved Domains Finding Homologs and Structures BLink: BLAST Link Redundant GIs BLink: non-redundant relatives top 200 only zebrafish homolog BLAST 5
6 Short Cut: Related Structures E. coli MutL Structure Structure Neighbors Cn3D viewer Pubchem compound 3D Domain Neighbors Conserved Domains MLH1 Domain Structure: CDD MLH1: ATPase Domain ATPase Domain Mismatch Repair Domain 6
7 GeneView: Variations Human MLH1 Mapping Polymorphisms onto Structure ATPase domain Related Structures Mapping Variation Onto Structure Asn Ile Ile Val Conserved Asn 7
8 NM_000249: Genome Links Genome Resources The Map Viewer Map Viewer: Human MLH1 Customizable Genome BLAST EST Hits Transcripts Download data and sequences Models NCBI Assembly Gene Annotations 8
9 Synteny: Mammalian Genomes orthologs Homologene paralogs orthologs Albumin Gene Family Completely Annotated Eukaryotic frog Genomes A chick A mouse A mouse B chick B frog B Homologous UniGene determined for other organisms Protein similarities first Guided A-chain by taxonomic gene tree B-chain gene Includes orthologs and paralogs gene duplication early globin gene Homologene Cluster Rice Homolog 9
10 The Gene Database Gene Centered Information Unifies LocusLink and microbial Genomes 2.4 million records for 3,822 taxa Genes MLH1: One Stop Shopping 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 MLH1: One Stop Shopping (cont.) Genes: Display Options and Links 10
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