FAQ

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SEED-FAQ: A list of Frequently Asked Questions about the SEED comparative environment.

  • Are the annotations in the SEED computer generated?

The subsystems based annotations in the SEED are created by a human expert, in contrast to many existing annotation approaches, the SEED annotation approach is to annotated a subsystems across many genomes at a time by an expert curator. Genes not in subsystems are annotated using an automatic decision procedure.


  • Is the SEED available?

Yes, the SEED is open source. Both our source code and the accompanying data are available. Please check our download site.


  • What genomes are included in the SEED data set?

This is a placeholder for a PAGE that has a pointer to our genomelist.


  • How often is the SEED updated?

The SEED is continuously updated, as new genomes are becoming available from the sequencing centers and/or NCBI's GenBank.


  • What is the difference between SEED, SEED-Viewer and Trail-SEED?

The SEED is a complex environment that is used for the comperative analysis of hudreds of genomes. It allows the annotation of sequence data, the integration and visualization of whole-genome data sets (e.g. metabolic reconstructions, microarrya data, essentiality data etc.) and most notably the creation of new and curation of existing subsystems. Our experienced curators and collaborators are using a master instance of the SEED. The SEED-Viewer is a user-friendly, browse-only interface to those curated genomic data sets. The Trail-SEED, a publicly writable copy of the SEED is available for testing purposes.


  • What is the difference between the SEED, the SEED-Viewer and the metagenomics SEED.

While the SEED is the curation platform for genomes, the SEED-Viewer is an application for viewing the data contained. The metagenomics SEED is a special purpose SEED installation for metagenomes.


  • What data is available inside the SEED-Viewer?

All data from the associated SEED database is available for exploration in the SEED-Viewer. The data underlying the SEED-viewer is updated on a nightly basis from the main curation machine. Work in progress is not made available on the SEED-Viewer, except for that the SEED-Viewer is a complete replicate of the main SEED server.


  • Can I link my web site to the SEED?

YES. We provide stable IDs for our genomes and genome features and a mechanism to construct hyperlinks.

The base URL:

http://link.theseed.org/linkin.cgi?id=

will link to the web page for a specific SEED data object.

Example:
 http://link.theseed.org/linkin.cgi?id=fig%7C83331.1.peg.2


  • On what platforms do you run SEED?

Our platforms are MacOSX (Intel and PPC) and Linux (Debian/RedHat/Fedora on Intel and PPC).


  • Can I annotate my genome with the SEED?

Yes, but only if your genome is included in the SEED. As of now, inclusion of genomes in the SEED can only be done in two ways, install a local instance and work with that or request inclusion of your genome via email. However we are planning to make available a genome annotation service based on SEED technology.


  • Are there other similar efforts out there?

Yes. Currently we are aware of TIGR's Comprehensive Microbial Resource (CMR) and JGI's Integrated Microbial Genomes (IMG).


  • What is the difference between SEED and other annotation approaches?

Annotations in the SEED are built on two main pieces of evidence, sequence similarity and conservation on the chromosome. Most other systems merely rely on sequence similarity. In addition to this, the SEED approach to annotation is based on the concept of having expert annotators curate subsystems of functionally related functional roles.