New Menu Structure
We have reorganized the menus in order to make it easier to find the key pages of the site.- The Home menu has links to the front pages of our three database web sites—SEED, NMPDR, and the Annotation Clearinghouse.
- The Annotate menu has links to our rapid annotation servers—RAST and MG-RAST.
- The Compare menu links to various tools for comparing genes and genomes.
- The Search menu has links to all of our database search tools.
- The Resources menu has links to pages of useful information for education or independent research.
- The Help menu has links to pages about how to use the NMPDR.
| 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. |
| 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. |
| Resources | |
|---|---|
| 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. |
| NewDevelopmentTemplateForm | |
|---|---|
| Date | 19 Jan 2009 |
| Title | New Menu Structure |
| Type | General |
Topic revision: r1 - 20 Jan 2009 - 00:44:19 - Bruce Parrello
Notice to NMPDR Users - The NMPDR BRC contract has ended and bacterial data from NMPDR has been transferred to PATRIC (http://www.patricbrc.org), a new consolidated BRC for all NIAID category A-C priority pathogenic bacteria. NMPDR was a collaboration among researchers from the Computation Institute of the University of Chicago, the Fellowship for Interpretation of Genomes (FIG), Argonne National Laboratory, and the National Center for Supercomputing Applications (NCSA) at the University of Illinois. NMPDR is funded by the National Institute of Allergy and Infectious Diseases, National Institutes of Health, Department of Health and Human Services, under Contract HHSN266200400042C. Banner images are copyright © Dennis Kunkel.