NCBI Field Guide NCBI Molecular Biology Resources Using
NCBI Field. Guide NCBI Molecular Biology Resources Using Entrez March 2007
Entrez & BLAST NCBI Field. Guide WWW Access
NCBI Field. Guide Entrez: Database Integration Word weight Pub. Med abstracts 3 -D 3 -D 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 Field. Guide Database Searching with Entrez u. Using limits and field restriction to find human Mut. L homolog u. Linking and neighboring with Mut. L u. Mapping SNPs onto structure and the genome
Human hereditary nonpolyposis colon cancer NCBI Field. Guide Global NCBI (Entrez) Search
NCBI Field. Guide Global Entrez Search Results
NCBI Field. Guide Nucleotide Sequences Nucleotide database now three parts • EST expressed sequence tags • GSS genome survey sequences • Core. Nucleotide everything else
Tabs NCBI Field. Guide Advanced Search Options
nonpolyposis[All Fields] AND colon cancer[Title] AND human[Organism] AND biomol_mrna[Properties] AND srcdb_refseq[Properties] NCBI Field. Guide More Precise Nucleotides Search
[Title]: Definition line in Gen. Bank / Gen. Pept 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 Field. Guide Useful Field Restrictions
NCBI Field. Guide Organism Field: NCBI’s Taxonomy
Molecule type biomol_mrna biomol_genomic Gen. Bank 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 Field. Guide Useful Properties Field Terms
Gen. Bank Records NCBI Field. Guide Human Mut. L Ref. Seq
NCBI Field. Guide NM_000249: Links
NCBI Field. Guide Literature Links OMIM
Conserved Domain NCBI Field. Guide OMIM: Human Disease Genes
NCBI Field. Guide Sequence Links Finding Homologs and Structures
BLAST Link Conserved Domains NCBI Field. Guide Protein Link
Redundant GIs top 200 only NCBI Field. Guide BLink: BLAST Link
zebrafish homolog BLAST NCBI Field. Guide BLink: non-redundant relatives
NCBI Field. Guide Short Cut: Related Structures
Structure Neighbors Pubchem compound Cn 3 D viewer 3 D Domain Neighbors Conserved Domains NCBI Field. Guide E. coli Mut. L Structure
ATPase Domain Mismatch Repair Domain NCBI Field. Guide MLH 1 Domain Structure: CDD
NCBI Field. Guide MLH 1: ATPase Domain
NCBI Field. Guide Mapping Polymorphisms onto Structure
NCBI Field. Guide Gene. View: Variations Human MLH 1 ATPase domain
NCBI Field. Guide Related Structures
Asn Ile – Val Conserved Asn Ile NCBI Field. Guide Mapping Variation Onto Structure
NCBI Field. Guide Genome Resources
NCBI Field. Guide NM_000249: Genome Links
Genome BLAST NCBI Field. Guide The Map Viewer
Customizable Transcripts EST Hits Download data and sequences Models NCBI Assembly Gene Annotations NCBI Field. Guide Map Viewer: Human MLH 1
Albumin Gene Family NCBI Field. Guide Synteny: Mammalian Genomes
orthologs paralogs orthologs • Completely Annotated Eukaryotic Genomes frog A chick A mouse B chick B frog B • Homologous Uni. Gene 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 Field. Guide Homologene
NCBI Field. Guide Homologene Cluster
NCBI Field. Guide Rice Homolog
• Gene Centered Information • Unifies Locus. Link 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 Field. Guide The Gene Database
NCBI Field. Guide Genes MLH 1: One Stop Shopping
(cont. ) NCBI Field. Guide Genes MLH 1: One Stop Shopping
NCBI Field. Guide Genes: Display Options and Links
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