Gramene User Help

Where does Gramene get its protein accessions from?

Gramene gets the protein accessions from Swissprot. (http://kr.expasy.org/sprot/)

What are some examples of scientific queries that can be answered using the Proteins database?

Users can research the molecular function, biological process and cellular location of a particular rice protein, find its sequence information, orthologs from other species, examine its physio-chemical features including its amino acid composition, examine which proteins are members of the same protein family (Pfam), determine if it is an enzyme, and also determine its location in the rice genome and examine neighboring genes and features. You can determine the name of the gene, its symbol, and if known, a link to the related phenotype listed in Gramene's Genes database.(http://www.gramene.org/rice_mutant/)

Is there a tutorial or help section on how to use the Proteins database?

Yes. Please refer to the Proteins Help page, tutorials, and release notes at http://www.gramene.org/tutorials/proteins.html.

From which grasses does Gramene have protein sets?

Gramene has the entire Poaceae(Grasses) family of Uniprot proteins. We are focusing on rice protein curation currently.

Can I search the Proteins database using a protein family (Pfam/Prosite) name or accession number?

Yes, you can do so by selecting "Search by Pfam or Prosite" from the Proteins (http://www.gramene.org/protein/index.html) database index page navigation bar or by using the advanced Protein search. (http://www.gramene.org/db/protein/protein_advanced)

Where can I find the sequence of a given protein?

You can do so by visiting the FASTA Sequence link in the secondary navigation bar found on top of the "General Information" section of a protein page of interest (view an example Protein page http://www.gramene.org/db/protein/protein_search?protein_id=78073)

How can I find out if a given protein is mapped to a gene from the rice genome?

You can find this information by looking in the Genomes field in the General Information section of a protein page of interest (view an example Protein page at http://www.gramene.org/db/protein/protein_search?protein_id=78073)

Where can I find the germplasm from where the gene encoding a given protein was isolated?

You can get this information by visiting a protein page of interest. Once there, look for the Cultivar field in the Organism section, under General Information (view an example Protein page at http://www.gramene.org/db/protein/protein_search?protein_id=78073)

Where can I find either the Molecular Function, Biological Process or Cellular Location of a given protein?

You can get this information by visiting the Association section of a protein page of interest (view an example Protein page at http://www.gramene.org/db/protein/protein_search?protein_id=78073)

What are the evidence codes used by Gramene in the Proteins database?

An explanation of Gramene's evidence codes can be found on the Evidence Codes page.(http://www.gramene.org/plant_ontology/evidence_codes.html)

Where can I find the experimental evidence that infers a gene ontology association to a protein?

You can find this by looking in the Evidence field in the Associations section on a protein page of interest (view an example Protein page (http://www.gramene.org/db/protein/protein_search?protein_id=78073").

Where can I find sequence homologs from other species?

You can find these by visiting the Similarity to Other Proteins" section of a protein page of interest (view an example Protein page (http://www.gramene.org/db/protein/protein_search?protein_id=78073).

How can I find out the protein family (PFam) to which a given protein belongs and also find all the proteins that belong to that family?

You can find the PFam information by visiting the Pfam field in the Protein Features section of a protein page of interest (view an example Protein page (http://www.gramene.org/db/protein/protein_search?protein_id=78073). In order to find all the proteins that belong to this protein family (PFam), click on the All Members of this Family in the Pfam field.

How can I find the protein domains (Prosite) of a given protein and also find all the proteins that carry that domain?

You can find the Prosite information by visiting the Prosite field in the Protein Features section of a protein page of interest (view an example Protein page (http://www.gramene.org/db/protein/protein_search?protein_id=78073). In order to find all the proteins that share this Prosite domain, click on All members of this Family in the Prosite field.

Where can I find the Physio-chemical features of a given protein?

You can find them by visiting the link in the Physio-chemical features" field in the Protein Features section of a protein page of interest (view an example Protein page (http://www.gramene.org/db/protein/protein_search?protein_id=78073").

Where can I find literature citations describing a given gene or protein?

You can find the references by visiting the References Used for Curation link in the navigation bar found on the top of the "General Information" section of a protein page of interest (view an example Protein page (http://www.gramene.org/db/protein/protein_search?protein_id=78073). Alternatively, scroll to the bottom of the protein page where you will find a list of the references that were used in the curation process. However, you will find more references by clicking on the button which says Search the Literature Database for Additional References. This returns a list of references using the gene name and symbol of interest to query the literature database.

What are the various options for downloading protein data?

You will find this information on the Proteins database index page (http://www.gramene.org/protein/#doc). The various download options are: -download a full list of Gene Ontology associations to the proteins -download sub cellular localization and transmembrane prediction analyses data -download all the rice sequences from Gramene/Swissprot/TrEMBL/GenBank or the rice (indica) sequences referred to in the article Yu et al. Science, 2002, 296, pp.79-92. (http://www.gramene.org/db/literature/pub_search?ref_id=6544) -use Gramene's Proteins ftp site to download protein features, ontology associations and sequences. (ftp://ftp.gramene.org/pub/gramene/CURRENT_RELEASE/data/protein/)