Navigating the NMPDR

Navigation Bar
Hierarchical Site Map

Navigation Bar

The navigation bar is located immediately underneath the banner at the top of each page. The table below lists each item in the bar along with a short description.

Home
NMPDR	Return to the home page for the NMPDR website.
SEED	Work with the public version of the SEED Environment for genome annotation.
Annotation Clearinghouse	Visit the Annotation Clearinghouse, a web database of assertions about features and protein encoding genes. You can upload your own assertions or view others.
Annotate
RAST	Use the Rapid Annotation Server to electronically annotate large Genomes. For more about this service, read our paper at FIG.BioMed Central.
MG-RAST	Use the Metagenomics Rapid Annotation Server, a variant of the RAST for metagenomes? .
Compare
Annotations	Display all the annotations submitted to the Annotation Clearinghouse for a selected genome.
Proteomes	Display a table of Bidirectional Best Hits between selected genomes. The table is color-coded so you can visualize the genetic distance between the organisms represented.
Subsystems	Compare the metabolic pathways used by two organisms.
Signature Genes	Find genes that are common among selected genomes or differentiate two sets of genomes.
FIGfams	Find the protein family of a FASTA Format amino acid sequence.
KEGG maps	View the KEGG diagrams for a particular genome.
Search
BLAST or Scan	Search for protein or DNA sequences using BLAST or our advanced pattern-scanning tool.
Genes	Search for genes in selected genomes using keywords, a specific subsystem, or both.
Organisms	View a summary of NMPDR core organisms and a list of supporting organisms.
Subsystems	View the tree of subsystems, and do keyword searches in individual subsystems or subsystem categories.

Resources
Protein Targets	Search for genes using a combination of useful criteria.
Batch ID Search	Find genes from an uploaded file of IDs.
Index of Search Tools	Select one of the Sprout Database search tools.
Publications	See a list of journal papers that reference the NMPDR.
Essential Genes	Explore genes determined to be essential in genome-wide screens.
Drug Targets Pipeline	Read about our drug target pipeline.
Teaching with NMPDR	View presentation materials and student assignments designed to use the NMPDR as a teaching tool.
Downloads	Download links for the NMPDR Core Genomes? .
NMPDR Source Code	View the documentation of the NMPDR source and access the download links.
Attributions	View a list of the tools and data sources used to build the NMPDR.
Cells, Reagents, Databases, Images	View links to databases of interest to the bionformatics? community.
Bioinformatics Resource Centers	Learn about the BRC project and the web sites that are participating in it.
Regional Centers of Excellence	View the ten regional centers established by the Biodefense and Emerging Infectious Diseases Research initiative.
Research Links	Search for information on general-interest and bioinformatics web sites.
Help
Where to Start	If you're new to the NMPDR, learn how to mine our Sprout Database and read examples of how to use this site to answer biological questions about DNA and proteins.
Glossary	Read our glossary of useful terms.
FAQ	See our answers to frequently asked questions.
Tutorials and Workshops	Learn how to use the NMPDR.
Help Index	Go to the home page for all our help materials.
SOPs	View our standard operating procedures.
Contact Us	View EMAIL and address information about the NMPDR staff.

Hierarchical Site Map

The NMPDR is divided into sections called webs, each with a different purpose. Inside each web, the pages are organized into a hierarchy, reflected in the breadcrumbs underneath the navigation bar. The major hierarchy of each web is shown in the tree below.

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Main Web: Resources for education and research, including search and data pages

FIG Web: Pages describing how the NMPDR works

Databases and Codes
- Aliases and Equivalent Genes: Notes on the notion of equivalence and how it relates to features and genes
- Cell Location Code: Regions of a cell in which proteins are expected to appear
- Custom Attributes Database: Diagram and description of the database used to store free-form data attributes
- DNA Nucleotide Code: Definitions of the four DNA nucleotides
  - Standard Ambiguity Code
- ERDB System: Entity-Relationship Database System
- Evidence Code: Codes that describe the evidence for the NMPDR's functional role assignments
- Habitat Code: Common organism habitats
- Oxygen Requirement Code: Code for an organism's behavior relating to oxygen.
- Salinity Code: Code for the behavior of an organism in relation to salt in its environment
- Sapling Database: Diagram and definition of the proposed successor to the Sprout Database?
- SEED Environment: The annotation software used by the NMPDR Genome Pipeline?
- Special Purpose Databases: Additional, related databases hosted by the University of Chicago
- Temperature Range Code: Code for the behavior of an organism in relation to the temperature of its environment
FIG Articles
Glossary
- Accession Number
- Alias
- Amino Acid Codes: Standard entry codes for protein sequences
- Annotation
- Assertion
- BLAST
- Bidirectional Best Hit
- CDS
- Clustering Based Subsystem
- Codon
- Conserved Domain Database
- Contig
- Core Organisms
- Domain
- EValue
- EC Number
- FASTA Format
- Feature
- Fellowship for Interpretation of Genomes
- FIGfam
- FIG ID
- Frame Shift
- Functional Coupling
- Functional Role
- GBK
- Genome
- Gram Stain
- Messenger RNA
- Metabolic Reconstruction
- Motif
- Ortholog
- PFAM
- PSORT
- Pair of Close Homologs PCH
- Paralog
- Protein Domain
- Protein Encoding Gene
- Ribosomal RNA
- Similarity
- Stop Codon
- Strand
- Subsystem
- Subsystems Approach
- Tar File
- Taxonomy Identifier
- Transfer RNA
- Variant
Grand Design
- Erdb Tutorial: Tutorial for the Entity-Relationship Database System
  - Asking for Gram Stain Data: A query that uses semi-booleans.
  - Erdb Benefits: What ERDB tries to do
  - Erdb Documentation Widget: Accessing database documentation via the ERDB Query Console
  - Erdb Entities Relationships Objects: Basics of Entity-Relationship Models
  - Erdb Naming Guidelines: The rules for object and field names
  - Erdb Overview Picture: Drawing of the ERDB components
  - Erdb Query Basics: A Simple Query Example
  - Exotic Data Types: Not everything is numbers, strings, and dates
  - Formulating a Query 1: Creating a simple query.
  - Formulating a Query 2: Adding the genome name to the query results
  - Formulating a Query 3: Making the query results easier to read
  - More Advanced Query: Starting from a feature instead of a family.
  - More Advanced Query That Works: Fixing the problem in the previous page.
  - Playing with the Doc Widget: Using the Documentation Widget
- Genome Pipeline: How new genomic data makes its way into the NMPDR database
- Genome Viewer: Instructions for using our genomic data portal
  - Compare Regions
  - Genome Viewer Annotation Page: Primary display page for individual features?
  - Interactive Table
  - Linking to the Genome Viewer
- Metagenomics Rapid Annotation Server: About the Rapid Annotation Server for Metagenomes
- NMPDR Banner: About the banner above every page
- NMPDR Website: Diagram of the NMPDR website
- Rapid Annotation Server: An introduction to our rapid genome annotation service
- Sprout Database: A diagram and description of the main NMPDR database
NMPDR Search

SOP Web: Standard Operating Procedures

Building a New Development NMPDR
Diagram Pages
Feature Annotation
Finding a Degenerate Peptide Motif In Selected Organisms
Finding Genes That Are Important In Specified Types of Pathogens
Finding Genes That May Be Characteristic of a Phenotype
Fixing NMPDR Content Errors
Importing Functional Coupling Data: Import functional coupling data for load into the Sapling Database
Importing Taxonomy Data
Installing a Sapling Database: Install and configure a Sapling database
Investigating an NMPDR Application Error
Kegg Map Update
NMPDR Lightweight Code Update
NMPDR Wiki Refresh
Producing the Monthly Statistics: Generate the data for the Counts and Statistics page.
Simple Tests: Links to pages that can be used to test NMPDR functionality
Staging a New NMPDR
Updating FIG Fams

Code Web: NMPDR Source Code documentation