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NCBI FieldGuide NCBI Molecular Biology Resources Using Entrez March 2007 Entrez & BLAST NCBI FieldGuide WWW Access NCBI FieldGuide Entrez: Database Integration Word weight PubMed abstracts 3 -D 3-D Structure Structure Taxonomy Genomes Phylogeny BLAST Neighbors Related Sequences Neighbors Related Structures Protein sequences Nucleotide sequences Hard Link VAST BLAST Neighbors Related Sequences BLink Domains 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 Human hereditary nonpolyposis colon cancer NCBI FieldGuide Global NCBI (Entrez) Search 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 Tabs NCBI FieldGuide Advanced Search Options nonpolyposis[All Fields] AND colon cancer[Title] AND human[Organism] AND biomol_mrna[Properties] AND srcdb_refseq[Properties] NCBI FieldGuide More Precise Nucleotides Search [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 Useful Field Restrictions NCBI FieldGuide Organism Field: NCBI’s Taxonomy 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 Useful Properties Field Terms GenBank Records NCBI FieldGuide Human MutL RefSeq NCBI FieldGuide NM_000249: Links NCBI FieldGuide Literature Links OMIM Conserved Domain NCBI FieldGuide OMIM: Human Disease Genes NCBI FieldGuide Sequence Links Finding Homologs and Structures BLAST Link Conserved Domains NCBI FieldGuide Protein Link Redundant GIs top 200 only NCBI FieldGuide BLink: BLAST Link zebrafish homolog BLAST NCBI FieldGuide BLink: non-redundant relatives NCBI FieldGuide Short Cut: Related Structures Structure Neighbors Pubchem compound Cn3D viewer 3D Domain Neighbors Conserved Domains NCBI FieldGuide E. coli MutL Structure ATPase Domain Mismatch Repair Domain NCBI FieldGuide MLH1 Domain Structure: CDD NCBI FieldGuide MLH1: ATPase Domain NCBI FieldGuide Mapping Polymorphisms onto Structure NCBI FieldGuide GeneView: Variations Human MLH1 ATPase domain NCBI FieldGuide Related Structures Asn Ile – Val Conserved Asn Ile NCBI FieldGuide Mapping Variation Onto Structure NCBI FieldGuide Genome Resources NCBI FieldGuide NM_000249: Genome Links Genome BLAST NCBI FieldGuide The Map Viewer Customizable Transcripts EST Hits Download data and sequences Models NCBI Assembly Gene Annotations NCBI FieldGuide Map Viewer: Human MLH1 Albumin Gene Family NCBI FieldGuide Synteny: Mammalian Genomes orthologs paralogs orthologs • 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 • Guided by taxonomic tree A-chain gene B-chain gene • Includes orthologs and paralogs gene duplication early globin gene NCBI FieldGuide Homologene NCBI FieldGuide Homologene Cluster NCBI FieldGuide Rice Homolog • 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 Cow 23, 677 Green Plants 76,847 Chicken 18, 469 Archea 74,627 Zebrafish 38, 594 Bacteria 168,802 1,361,390 NCBI FieldGuide The Gene Database NCBI FieldGuide Genes MLH1: One Stop Shopping (cont.) NCBI FieldGuide Genes MLH1: One Stop Shopping NCBI FieldGuide Genes: Display Options and Links
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