theseed.org
SpecialPurposeDBs - TheSeed
http://www.theseed.org/wiki/SpecialPurposeDBs
Home of the SEED. EGGS database: Essential Genes on Genome Scale. Retrieved from " http:/ / /w/index.php? Home of the SEED. Scan for Matches (patscan). FAQ Frequently Asked Questions. This page was last modified on 6 January 2009, at 10:39. This page has been accessed 10,509 times.
theseed.org
Annotating 1000 genomes - TheSeed
http://www.theseed.org/wiki/Annotating_1000_genomes
Home of the SEED. A manifesto written in early 2004. The Project to Annotate the First 1000 Sequenced Genomes, Develop Detailed Metabolic Reconstructions, and Construct the Corresponding Stoichiometric Matrices. The Project to Annotate 1000 Genomes. We now proceed to describe the details of the three stages. Stage 1: Development of Initial Encodings of Subsystems. Stage 2: The Use of True Experts and the Wet Lab to Refine the Encodings. Filling in the Missing Pieces. The Project to Annotate 1000 Genomes.
theseed.org
Glossary - TheSeed
http://www.theseed.org/wiki/Glossary
Home of the SEED. Assigning a gene function and annotation. Bidirectional Best Hit (BBH). FIG Identifier / FIG-IDs. Linking to the SEED. Pair of Close Homologs (PCH). Usually used in context of feature IDs. They are database crossreferences. The master copy for all data in the SEED environment. Users can not access this password protected site. All annotations are made available via the SEED-Viewer. Please see Assigning a gene function and annotation. Assigning a gene function and annotation. A feature i...
theseed.org
Home of the SEED - TheSeed
http://www.theseed.org/wiki/Home_of_the_SEED
Home of the SEED. Home of the SEED. With the growing number of available genomes, the need for an environment to support effective comparative analysis increases. The original SEED Project was started in 2003 by the Fellowship for Interpretation of Genomes (FIG). Flow of data in the SEED. Curation of genomic data ( annotation. Is done via the curation of subsystems. By an expert annotator across many genomes, not on a gene by gene basis. This is also detailed in our manifesto. Also see our DownloadPage.
theseed.org
SEED Viewer Tutorial - TheSeed
http://www.theseed.org/wiki/SEED_Viewer_Tutorial
Home of the SEED. Selecting Browse annotated genome in SEED Viewer from the Job Details page of the RAST server will direct the user to the Organism Page in the SEED Viewer. Organism Page in SEED Viewer. In the navigation bar at the top of the page adjacent to the homepage symbol is a pull down menu labeled 'This Organism' with the following 4 display options for this page:. Figure 1. SEED Viewer navigation bar with links to the genome browser, genome features, reactions, and genome comparison tool.
theseed.org
DownloadPage - TheSeed
http://www.theseed.org/wiki/DownloadPage
Home of the SEED. This is the main SEED download page. All tools and datasets that make up the SEED are in the public domain and can be downloaded at ftp:/ ftp.theseed.org. Retrieved from " http:/ / /w/index.php? Home of the SEED. Scan for Matches (patscan). FAQ Frequently Asked Questions. This page was last modified on 18 August 2007, at 08:47. This page has been accessed 26,337 times.
theseed.org
SEED People - TheSeed
http://www.theseed.org/wiki/SEED_People
Home of the SEED. The people behind SEED are the following:. Mathematics and Computer Science Department. University of Illinois at Urbana-Champaign. Gary J. Olsen. Retrieved from " http:/ / /w/index.php? Home of the SEED. Scan for Matches (patscan). FAQ Frequently Asked Questions. This page was last modified on 14 January 2009, at 18:39. This page has been accessed 47,910 times.
theseed.org
SOPs - TheSeed
http://www.theseed.org/wiki/SOPs
Home of the SEED. SEED standard operating procedures. To generate data that is useful to the various communities involved in the process of annotation and use of annotations, we make available our standard operating procedures. Annotation Codes (NMPDR SOP010) File:Annotation sop.pdf. Annotating a genome with the 48-hour service (NMPDR SOP005) File:The48hrserver.pdf. Creation of GO-terms (NMPDR SOP004) File:GO AND PFAM SOP.pdf. Releasing GFF3 files(NMPDR SOP006) File:Brc upload sop.pdf. Home of the SEED.
