50 Recent Changes in FIG Web retrieved at 16:15 (GMT)
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 ...
Searching for Genes with Specific FunctionalRoles Using Keyword Seach There is no specific NMPDR search for genes by functional role; however, the functional ...
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 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 ...
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 ...
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 ...
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 ...
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 ...
HOPS Database (Hypotheses and Open Problems revealed by Subsystems) Sequencing and analysis of hundreds, soon to be thousands, of genomes reveals multiple gaps in ...
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 ...
The FIG Web This section of the site contains information to help you understand and use the NmpdrWebsite. Contents Glossary our terminology Grand ...
This section contains information about the data available on the NmpdrWebsite.
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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 ...
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 ...
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 ...
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 ...
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 ...
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 ...
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 ...
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 ...
RAST: the Rapid Annotation Server RAST (Rapid Annotation using Subsystem Technology) is a fully automated service for annotating bacterial and archaeal genomes ...
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 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 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 ...
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 ...
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 ...
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 ...
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 ...
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 ...
14 Aug 2008
If you are a returning user you will have probably noticed the radical change in the interface of the new NMPDR. 14 Aug 2008
FIG Web Preferences The following settings are web preferences of the FIG web. These preferences overwrite the site level preferences in . and , and ...
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 ...
29 May 2008
New Developments Organism News Articles 29 May 2008
29 May 2008
29 May 2008
Protein encoding gene (PEG), protein coding sequence (CDS), and open reading frame (ORF) are synonymous terms. Protein encoding genes are commmonly described as structural ...
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 ...
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 ...
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 ...
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 ...
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 ...
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 ...
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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.