NCBI Molecular Biology Resources

1
NCBI Molecular Biology Resources
David Landsman landsman_at_ncbi.nlm.nih.gov
September 2006
2
WWWAccess
Entrez BLAST
3
Entrez Database Integration
Word weight
PubMed abstracts
3-D Structure
3 -D Structure
Taxonomy
VAST
Genomes
Phylogeny
Neighbors Related Structures
Protein sequences
Nucleotide sequences
BLAST
BLAST
Neighbors Related Sequences BLink Domains
Neighbors Related Sequences
Hard Link
4
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

5
Global NCBI (Entrez) Search
6
Global Entrez Search Results
7
Nucleotide Sequences

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

8
Advanced Search Options
Tabs
9
More Precise Nucleotides Search
nonpolyposisAll Fields AND colon cancerTitle
AND humanOrganism AND biomol_mrnaProperties
AND srcdb_refseqProperites
10
Useful Field Restrictions
Title Definition line in GenBank / GenPept
format shown in Summary format glyceraldehyde 3
phosphate dehydrogenaseTitle Organism
NCBIs taxonomy. Organizing system for molecular
databases mouseorganism green
plantsorganism Streptomyces coelicolororganism
Properties molecule type, location,
database source biomol_mrnaproperties
biomol_genomicproperties gene_in_mitochondrion
properties srcdb pdbproperties Filter
subsets of data, Entrez links allfilter
nucleotide mapviewfilter nucleotide
omimfilter
11
Organism Field NCBIs Taxonomy
12
Useful Properties Field Terms
13
Human MutL RefSeq
14
NM_000249 Links
15
Literature Links

• OMIM

16
OMIM Human Disease Genes
17
Sequence Links

• Finding Homologs and Structures

18
Protein Link
BLAST Link
Conserved Domains
19
Related Proteins Homologs and Redundancy
Redundant Sequences
20
BLink BLAST Link
top 200 only
21
BLink non-redundant relatives
zebrafish homolog
BLAST
22
Related Protiens Structure Links
23
Structures
24
Short Cut Related Structures
25
E. coli MutL Structure
Cn3D viewer
Structure Neighbors
3D Domain Neighbors
Pubchem compound
Conserved Domains
26
MLH1 Domain Structure CDD
Mismatch Repair Domain
ATPase Domain
27
MLH1 ATPase Domain
28
Mapping Polymorphisms onto Structure
29
Entrez SNP
"coding nonsynon"Function Class
30
GeneView Variations Human MLH1
31
Related Structures
32
Mapping Variation Onto Structure
Asn
Ile
Conserved Asn
Ile Val
33
Genome Resources
34
Higher Genome Resources
35
Microbial Genomes
36
NM_000249 Genome Links
37
The Map Viewer
Genome BLAST
Previous Builds Available
38
Map Viewer Human MLH1
Customizable
EST Hits
Transcripts
Models
NCBI Assembly
Gene Annotations
39
Maps and Options
40
Mapped Variations
41
Synteny Mammalian Genomes
42
The New Homologene

• No longer UniGene based
• Protein similarities first
• Guided by taxonomic tree
• Includes orthologs and paralogs

43
The New Homologene
44
Rice Homolog
45
The Gene Database

• Gene Centered Information
• Unifies LocusLink and microbial Genomes
• 1.8 million records for 3,262 taxa

46
Genes MLH1 One Stop Shopping
47
Genes MLH1 One Stop Shopping (cont.)
48
Genes Display Options and Links