NCBI FieldGuide

Using Entrez

An integrated database
search and retrieval system
 NCBI FieldGuide
WWW
Access

Entrez
&
BLAST
 Entrez: Database Integration
Word weight

PubMed
abstracts

Taxonomy 3 -D
3-D
Structure
Structure
VAST

Phylogeny Genomes

Nucleotide Protein
BLAST BLAST
sequences sequences
 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
Global Entrez Search

NCBI FieldGuide
Document Summaries:

NCBI FieldGuide
MutL[All Fields]
Entrez Nucleotides: Limits & Preview/Index

NCBI FieldGuide
Tabs
 Entrez Nucleotides: Limits
Accession
All Fields

NCBI FieldGuide
Author Name
EC/RN Number
Feature key
Filter
Gene Name Field Restriction
MutL Issue
Journal Name
Keyword
Modification Date
Organism Exclude bulk sequences
Page Number
Primary Accession
Properties
Protein Name
Publication Date
SeqID String
Sequence Length
Substance Name
Text Word
Title
Uid
Volume
 Entrez Nucleotides: Limits

NCBI FieldGuide
MutL

Title == Definition

Exclude Bulk Sequences

Document Summaries: Limits

NCBI FieldGuide
Adding Terms: Preview/Index

NCBI FieldGuide
Accession
All Fields
Author Name
EC/RN Number
Feature key
Filter
Gene Name
Issue
Journal Name
Keyword
Modification Date
Organism
Page Number
Primary Accession
Properties
Protein Name
Publication Date
SeqID String
Sequence Length
Substance Name
Text Word
Title
Uid
Volume
Human MutL Search Results

NCBI FieldGuide
 Human MutL RefSeq

NCBI FieldGuide
GenBank Records
NM_000249: Links

NCBI FieldGuide
 NCBI FieldGuide
Literature Links

PubMed
OMIM
NM_000249: PubMed

NCBI FieldGuide
Books
 NCBI FieldGuide
Books Link
OMIM: Human Disease Genes

NCBI FieldGuide
Conserved Domain
 NCBI FieldGuide
Sequence Links

Nucleotide Protein
NM_000249: Related Sequences

NCBI FieldGuide
Genome Project BAC

similarity
Original GenBank mRNAs

Original GenBank genomic

 NCBI FieldGuide
Taxonomy Link

The Tax Browser

NCBI’s Taxonomy
 NCBI FieldGuide
Taxonomy Link
 NCBI Protein Databases

NCBI FieldGuide
• GenPept GenBank, EMBL, DDBJ CDS translations
• RefSeq mRNA based (NP_) and genome based (XP_)
• Swiss-Prot curated high quality protein reviews
• PIR protein information resource Georgetown University
• PRF protein resource foundation
• PDB Protein Databank sequences from structures
Protein Link

NCBI FieldGuide
BLAST Link

Conserved Domains
 NCBI FieldGuide
Related Proteins: Redundancy

Redundant Sequences
Related Proteins: Links

NCBI FieldGuide
Sequence from MutL structure
BLink: non-redundant relatives

NCBI FieldGuide
Arabidopsis homolog

Conserved Domain
 MLH1 Domain Structure: CDD

NCBI FieldGuide
ATPase Domain Mismatch Repair Domain
MLH1: ATPase Domain

NCBI FieldGuide
ATPase structural alignment

NCBI FieldGuide
ATP Binding site helix
Variations Human MLH1

NCBI FieldGuide
 BLink

NCBI FieldGuide
Finding structural models
 Mapping Variation Onto Structure

NCBI FieldGuide
Loads sequence alignment and structure in Cn3D

Bacterial DNA mismatch repair proteins

Mapping Variation Onto Structure

NCBI FieldGuide
Asn
Ile

Ile – Val Conserved Asn

 NCBI FieldGuide
Genome
Resources
NM_000249: Genome Links

NCBI FieldGuide
Higher Genome Resources

NCBI FieldGuide
MLH1: UniGene Cluster

NCBI FieldGuide
ESTs in UniGene

NCBI FieldGuide
The Map Viewer

NCBI FieldGuide
Genome BLAST page
Map Viewer: Human MLH1

NCBI FieldGuide
Customizable Annotation
EST Hits

Models

NCBI Assembly

Gene Annotations
Maps and Options

NCBI FieldGuide
Synteny: Mammalian Genomes

NCBI FieldGuide
 The New Homologene

NCBI FieldGuide
orthologs
• No longer orthologs
UniGene based
paralogs
• Protein similarities first
• Guided by taxonomic tree
frog A chick A mouse A mouse B chick B frog B
• Includes orthologs and paralogs

A-chain gene B-chain gene

gene duplication

early globin gene

The New Homologene

NCBI FieldGuide
C.elegans homolog

NCBI FieldGuide
 NCBI FieldGuide
Microbial
Genomes
Related Proteins->Genome Links

NCBI FieldGuide
 NCBI FieldGuide
Genome Links
Microbial Genomes

NCBI FieldGuide
COGs Analysis

NCBI FieldGuide
E.Coli K12 Genome
Entrez Genes: integrated gene-based access

NCBI FieldGuide
LocusLink
Complete Genomes
•eukaryotic
•microbial
•organelle
Genes MLH1: Central Resource

NCBI FieldGuide