Results from FIG web retrieved at 06:44 (GMT)
If you are a returning user you will have probably noticed the radical change in the interface of the new NMPDR. 14 Aug 2008
An alias is a gene identifier from an outside organization or database. Inside the NMPDR's data structures, the FigId is used for each gene. Each gene also has a list ...
Basic Concepts In the NmpdrWebsite and SeedEnvironment databases, there is a general concept of a piece of DNA. In the databases and in the SEED, this is called a ...
The Annotation Clearinghouse Services Provided by the Annotation Clearinghouse The Annotation Clearinghouse is a rather simple web site that collects Assertions ...
The AnnotationClearinghouse was introduced to support two services. The basic service allows the user to ask for all of the function annotations for a specified protein ...
29 May 2008
An assertion is a statement about the purpose of a particular feature in a genome . The most common type of assertion is the assignment of a FunctionalRole ...
var stuff ""; function GetDiagramData() { return stuff; } stuff '/FIG/AttributeDatabase, /, ';
Introduction The Attributes Database allows applications to upload and retrieve custom data for NMPDR data objects. It uses the ERDB database system (which is also ...
Name Type Size Values Tooltip message Attributes Original Author select values M Display Title text 40 Title for this ...
BBH example: the black arrows represent best hits. The best hit of a particular gene to a target genome is the gene in that genome that represents a best ...
NMPDR is a Bioinformatics Resource Center. Each center specializes in certain pathogens. In NMPDR, we call these the core genomes or NMPDR genomes . The genomes ...
The DNA nucleotide codes describe the four base compounds that make up a DNA sequence. The codes are as follows. Name Letter Type Pairs With Formula ...
This section contains information about the data available on the NmpdrWebsite.
One of the projects underway at the NMPDR is generating in silico docking results for proteins that are believed to be good drug targets. For each selected protein ...
FASTA format is a standard format for encoding DNA or protein sequences. A FASTA file generally contains one or more sequences in FASTA format. A single sequence ...
Features and Genes A feature is anything that can be mapped onto a strand of DNA, and is defined by its start and stop location. Feature is a catch all, general ...
The Fellowship for Interpretation of Genomes (FIG) FIG is a nonprofit organization devoted to providing support for those analyzing genomes . Sequencing of genomes ...
This is the default template for creating a FIG Article. Fig Articles are papers about the projects undertaken by the Fellowship for Interpretation of Genomes ...
Master List of Articles Last Changed Original Author Title Excerpt
FigFams are sets of ProteinSequences that are similar along their full length. Proteins are thought of as implementing one or more abstract FunctionalRoles. All of ...
FigFams: Yet Another Set of Protein Families What Are the FigFams? Each individual FigFam is a set of protein sequences, along with a decision procedure. All of ...
Every gene in the NMPDR database has a unique FigId. It has four parts, as shown in the diagram below. /FigID.png The prefix identifies the fact that this ...
This topic displays a table that helps people get Flash Player to work in their browser. This page requires Flash Player in order to display properly. if (navigator ...
The functional role of a feature is the task it performs in the host organism. The role is stored in the NMPDR database as a descriptive phrase. Some functional ...
The gene display options control the display of genes in the NMPDR Search Results . /GeneDisplayOptions.png If Sort by Function is checked, the search output ...
The gene search allows you to search for features in a specific set of organisms. Use the GenomeControl to select the organisms you want to search. Specify search ...
Screen shot from the GenomeViewer showing a section of genome A genome is a related collection of DNA. In most cases, a genome represents the DNA for a single sequenced ...
The Genome Control is a powerful tool for selecting one or more genomes . It lists every genome available in the NMPDR. The NMPDR core organisms are shown first ...
The Genome Pipeline A rapid annotation tool and a central clearinghouse for annotation data help to keep the NMPDR fresh. Data from the global community (green) flows ...
The Genome Viewer Introduction The Genome Viewer (also known as the SEED Viewer ) is our window into the various genetic data bases on the NmpdrWebsite. It comes ...
Glossary of Useful Terms
The Grand Design is a pictorial guide to the NmpdrWebsite and its related components. You will need the Adobe Flash Player to view the individual pages.
For instructions on how to create diagrams using this template, go to DiagramPages. If it becomes necessary to change this topic, then it may also be necessary to ...
Two features are said to be similar or homologous if they share a nearly identical DNA sequence. Two similar features are called homologs , and the set of one ...
How to Annotate a Genome We at the FellowshipForInterpretationOfGenomes (FIG) have actively led the ProjectToAnnotate1000Genomes since its inception in 2003. In that ...
How to Evaluate and Compare Genomes: A Proposal Introduction I was asked to defend the proposition that the annotation provided on the NmpdrWebsite adds significant ...
In each search form, the Identifier Type dropdown box, shown below, can be used to determine how feature IDs will be displayed in the search results. Normally ...
The NMPDR keyword search works like a typical search engine. You type in the appropriate words, and a list of genes will come back. Our keyword database contains millions ...
We support linking to the GenomeViewer using a generic mechanism via the base URL The linkin.cgi script provides a short, unified mechanism for getting into ...
MG RAST: The Metagenomics Rapid Annotation Server The Metagenomics RAST server is a modified version of the RAST Server designed specifically to work with metagenomes ...
This page contains a list of the pages in this web that are referenced, but do not yet exist.
A protein motif is a small section of a protein that has a known function, is folded independently of the rest if the protein, or functions as a docking site. The ...
29 May 2008
New Developments Organism News Articles 29 May 2008
At the top of every page is a banner containing a search box, a graphic logo, and a navigation bar. The actual graphic logo used depends on the width of your display ...
The NMPDR search facility provides many different ways to look for genes, genomes, or sequences in the NMPDR database. The following searches are currently supported ...
This topic lists the help pages for the search facility controls.
This topic lists the different types of database searches available on the NmpdrWebsite.
The GenomePipeline shows how information gets into the NMPDR. This diagram shows how it gets out. At the very top are the three main content sections of the NMPDR ...
The operon search displays features from a single genome in operon order . Features that are reasonably close to each other on the same strand are displayed ...
29 May 2008
Name Login Group This table lists the eligible authors for FigArticles.
Introduction In December, 2003 The Fellowship for Interpretation of Genomes (FIG) initiated The Project to Annotate 1000 Genomes. The explicit goal was to develop ...
The Attribute Search is used internally for testing purposes and to produce reports required by several of the web pages. If you found it, then you are probably following ...
Protein encoding gene (PEG), protein coding sequence (CDS), and open reading frame (ORF) are synonymous terms. Protein encoding genes are commmonly described as structural ...
RAST: the Rapid Annotation Server RAST (Rapid Annotation using Subsystem Technology) is a fully automated service for annotating bacterial and archaeal genomes ...
I have recently been reflecting on the status of the Project to Annotate 1000 Genomes and in this short essay I will argue that it has been an overwhelming success ...
Introduction The Sapling database is a distributable, self contained copy of the NMPDR data. Unlike Sprout, which is optimized for searching, Sapling is designed to ...
The Sapling database is a portable database that covers three realms of bioinformatics . It is currently a work in progress and subject to change; however, one ...
The results from an NmpdrSearch are displayed in a table, as shown below. /SearchResultImage.png Buttons in the result tables will generally take you to other pages ...
Searching for Genes with Specific FunctionalRoles Using Keyword Seach There is no specific NMPDR search for genes by functional role; however, the functional ...
Use the signature genes tool to find genes that are common among one set of genomes , or differentiate one set from another. Like most searches in the NMPDR ...
Introduction Entities Contig A contig is a contiguous run of nucleotides. The contig #39;s ID consists of the genome ID followed by a name that identifies which ...
HOPS Database (Hypotheses and Open Problems revealed by Subsystems) Sequencing and analysis of hundreds, soon to be thousands, of genomes reveals multiple gaps in ...
Introduction The Sprout database contains the genetic data for all complete organisms in the SeedEnvironment. The data that is not in Sprout attributes, similarities ...
The Sprout database contains 34.6 billion characters of data and and additional 2.8 gigabytes of search indexes. The main tables are shown in the diagram below. Rectangles ...
The standard ambiguity codes can be used to represent sets of possible values in a DNA sequence. Code Nucleotides M {A, C} R {A, G} W {A ...
Subsystems are organized in broad functional categories. The subsystem search tool displays the subsystems and their categories in the form of a tree, as shown below ...
Subsystem diagram for , an example of a subsystem based on a metabolic pathway. Subsystems are a generalization of the concept of pathways, and they have two components ...
The subsystem filter is a dropdown menu on a search form that contains a list of subsystem names. It allows you to restrict the output to the features found ...
14 Aug 2008
The sequence search is designed to locate matching DNA or protein sequences among selected genomes in the NMPDR database. It includes three BLAST tools and two ...
NMPDR's FIG web
The FIG Web This section of the site contains information to help you understand and use the NmpdrWebsite. Contents Glossary our terminology Grand ...
FIG Web Preferences The following settings are web preferences of the FIG web. These preferences overwrite the site level preferences in . and , and ...
" else "NMPDR's FIG web"}% /FIG
Statistics for FIG Web Month: Topic views: Topic saves: File uploads: Most popular topic views: Top contributors for topic save and uploads ...
Local VIEW TEMPLATE WebCreateNewTopic
This is the default edit template for the FIG section. It is absent the signature used in the site default template. BruceParrello 21 Jan 2008
The Word Search is a bare bones search tool that searches all of the genomes in the NMPDR database using keywords entered in a KeywordBox. The standard GeneDisplayOptions ...
Number of topics: 105
See also the faster WebTopicList Topic revision: r4 - 15 Nov 2006 - 19:43:52 - TWikiContributor
NMPDR is 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.