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Frequently Asked Questions Questions General What is plantsUBQ? Where does PlantsUBQ get its protein/DNA/RNA information? Why is there a Master Gene List while I can search by keywords? How often is PlantsUBQ updated? How will I know when data have been updated? How is the data curated at PlantsUBQ? How many plant species are included in the database? What is your naming guideline for a particular entry? Do you assign GO term for a protein? How can I contribute to the database? What if I forget my password? How to use the PlantsUBQ database How to use the "User Preferences"? How to search for all Ubiquitin enzymes? How to get the DNA/RNA information of a protein sequence? How to generate XML file of selected proteins? What is the "Citations" link for? Against which database can I do a BLAST query? How to get a fasta file of multiple protein sequences? How to get a fasta file of multiple DNA/RNA sequences? How to make multiple alignments of proteins/DNA/RNA? How to compare multiple protein feature diagrams? How to compare multiple gene models? How can I find protein sequences containing certain motifs? How can I find out if my protein sequence contains certain motifs using your website? How to get more information about a particular motif on the protein feature diagram? How to find the meaning of A particular Acronym? How can I access other resources from PlantsUBQ website for a particular protein? Answers General What is plantsUBQ? PlantsUBQ is a database that provides a source of information for researchers studying Ubiquitin/26S Proteasome Proteolytic Pathway in Plants. This includes news, recent papers, colleague infromation, research progress, and much more. Where does PlantsUBQ get its protein/DNA/RNA information? We download data from major sources such as GenBank, PIR, EMBL, PRF, Swiss-Prot, At-genome, TIGR, TAIR, and SGD. Why is there a Master Gene List while I can search by keywords? The Master Gene List contains our best curated entries from the participating labs of the 2010 Project. We get first-hand information from those labs and update our database. How often is PlantsUBQ updated? Generally speaking, the data curation is a continuous process. As for sequences and gene model, we update our database whenever new release is out from major sources such as TIGR or TAIR. How will I know when data have been updated? There are two ways to find out: The first is to check the Chronology at the bottom of the detail page for the selected entry. The Revision history shows the time when changes were made. It may be a merging or updating. The second is to look at the Protein History and Links to Sources. The Current Entry shows the most recent data, including current sequences and their sources (e.g., TIGR-Ath5 means the entry is from TIGR release 5). How is the data curated at PlantsUBQ? We keep close contact with participating labs and update the data as new information comes in. We keep an eye on newly published papers and extract/integrate relevant information into our database annotation. Periodically we run queries to search for possible duplicates by running BlastN/BlastP against the database itself. After putting together a candidate merging list, we carefully double check the validation by examining name and synonyms, source entries, and the Blast alignments before the merge. How many plant species are included in the database? There are plant 100+ species in PlantsUBQ database. The best curated species are Arabidopsis thaliana and Oryza sativa. What is your naming guideline for a particular entry? For a particular entry, the name from the downloading source was used initially. When merging duplicate entries from different sources, the most common name is picked among all the synonyms to be the final entry name. For Arabidopsis thaliana, AGI number is the choice if no common name is available. Do you assign GO term for a protein? We do not have GO term associated with every entry in PlantsUBQ database. However, for newly annotated protein entries, we provide GO term lookup function for annotators. So hopefully we'll assign more PlantsUBQ entries with GO terms. How can I contribute to the database? You can contribute to the database by being an annotator. We have two portals that lead you to the annotation page: the first one is the "Annotate this entry" link in red on the multiple results page. The second portal is the "Start a discussion to annotate this protein" in the "Community Annotations" section on the detail page. Remember, you need register first in order to be able to contribute annotation. What if I forget my password? Just send us your username and your email account used for registration, and we'll send your password to that email account. How to use the PlantsUBQ database How to use the "User Preferences"? The "User Preferences" is mainly for two purposes right now (after registration): First, you can add selected entries to your "favorite" list. The "favorite" protein addition can be done either from the multiple result page by checking the target entry and selecting the "Add to favorites" option from the dropdown list, or can be done from the detail page by clicking on the "Add to your list of favorites" link (with a heart shape) in the Chronology section. Second, You can change your password and contact information through the "User Preferences" page. How to search for all Ubiquitin enzymes in Arabidopsis thaliana? To get the most accurate results, search by "PUBQC:UBQ" or click on the Ub icon on the image map on the homepage. We put "PUBQC:" before "UBQ", "E1", "E2" and "E3" in the keywords field if the entries are on the Master Gene List. This approach is used to distinguish the Master Gene List entries from other less curated entries. How to get the DNA/RNA information of a protein sequence? Click on the "RNA/DNA" link before the "General Information" section on the detail page. How to generate XML file of selected proteins? Click on the "XML" link before the "General Information" section on the detail page, or the "XML" link for each entry on the multiple results page. What is the "Citations" link for? The "Citations" link on the detail page will allow you to access the source reference where the sequences were extracted. Against which database can I do a BLAST query? The database options on the drop-down Database list allow you to do BLAST query based on your needs. For example, if you have no idea what a protein does, the "All Arabidopsis Proteins" or the "All Rice Proteins" will give you the original information about the sequence from TIGR even though the protein may not be in our PlantsUBQ database. Querying against the "PlantsUbq Proteins" will find the good matches in the PlantsUBQ database. How to get a fasta file of multiple protein sequences? On the multiple results page, check the target protein sequences, select the "FASTA Protein Sequence" option from the drop-down list on the top of the page, then click on "Make It So". Note: Currently you may select up to 160 sequences. How to get a fasta file of multiple DNA/RNA sequences? See previous answer for multiple protein sequences. Select "FASTA mRNA sequence" or "FASTA genomic sequence" accordingly. Don't forget to click on the "Make It So" button. How to make multiple alignments of proteins/DNA/RNA? On the multiple results page, check the target protein sequences, select the "Multiple Protein (or 'DNA', 'RNA') Alignments" option from the drop-down list on the top of the page, then click on "Make It So" - it will lead you to the EMBL-EBI ClustalW web interface to do the alignments. How to compare multiple protein feature diagrams? On the multiple results page, check the target protein sequences, select the "Protein Feature Diagram" option from the drop-down list on the top of the page, then click on "Make It So". How to compare multiple gene models? On the multiple results page, check the target protein sequences, select the "Exon-Intron Diagram" option from the drop-down list on the top of the page, then click on "Make It So". How can I find protein sequences containing certain motifs? On the Advanced Search page, clicking on "FIND" for the "Motif/Domain Search" will lead you to the "Search For Proteins by Presence of Features" page. The page provides simple instructions and a "more help" link. How can I find out if my protein sequence contains certain motifs using your website? On the Advanced Search page, clicking on "SCAN" for the "Motif/Domain Scan" will lead you to the "Scan for Motifs/Domains" page. Copy and paste your protein sequence in the "Protein sequence" area, select the source of Motifs/Domains, and click "Scan". How to get more information about a particular motif on the protein feature diagram? You can access detailed information about the feature and the method by clicking on the colored legends BELOW the protein feature diagram on the detail page. Clicking on the colored blocks ON the protein feature diagram will give you information about the particular feature instance as well. How to find the meaning of A particular Acronym? Choose "Advanced Search" on the menu of the homepage, then click on "Go to Lexicon" button to look up the term. How can I access other resources from PlantsUBQ website for a particular protein? The links in the "External Resources" section at the bottom of entry detail page will lead you to the corresponding protein entry in other resources if awailable.

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