Frequently Asked Questions

Questions

• What is dictyBase?
• How do I send a message to the Dicty community?
• How do I subscribe to the Dicty Listserv?
• How do I submit an abstract for publication in the dictyNews?
• How can I find a gene?
• What is a Gene Page?
• How do I find publications that are associated with a gene?
• Why should I reserve a gene name?
• What is curation?
• What is the chromosome 2 duplication?
• What are the XXX in a BLASTP alignment?
• What are BF, 2F, and 3F chromosomes?

This section will answer some questions about dictyBase. For further information on specific tasks and functions in dictyBase please consult the Help File Index. The respective specific "Help Documents" are also linked by a blue question mark from each page.

• What is dictyBase?
  dictyBase is a database that provides a centralized source of Dictyostelium information for Dictyostelium researchers and Non-Dictyostelium researchers. This includes tutorials, dictyNews, techniques, the Stock Center, genomic and molecular information, colleague infromation, Dictyostelium literature, and much more. Scientific curation makes this database especially valuable.
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• How do I send a message to the Dicty Community?
  Send your message to dicty@listserv.it.northwestern.edu. However, in order to receive the answers that people send to the ListServ you need to become a dictybase colleague (see below).
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• How do I subscribe to the Dicty Listserv?
  In order to subscribe to the Listserv you need to be in our "Colleague Database". This is why you enter the process through the "Colleague" link.
  1. Click on the "Colleague" button on the top bar.
  2. Enter your last name and click 'search'. If you are already in the Colleague Database choose your name from the list and click "Edit". This leads to the 'Update Form'. If you don't find your name, you will get a link on the next page 'Add New Colleague' to get a new 'Colleague Submission Form'.
  3. On either form, fill in at least the required fields. Make sure to enter your correct e-mail address. Most importantly to subscribe to the Listserv, make sure "Yes"on top of the form is selected (Would you like to subscribe to dictyNews?; Y by default).
  4. After you have entered your information, click "Continue at the bottom of the page, and "Submit" on the next page.
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• How do I submit an abstract for publication in the dictyNews?
  There is a link on the side bar (Abstract Submission) that leads to a form where you can paste your abstract. Alternatively, you can send your abstract to dicty@northwestern.edu.
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• How can I find a gene?
  The search box at the top of every page can be used to search for any gene name, alias, gene product, or GenBank accession number. The wildcard character (*) can be used to broaden the search. This will lead to a list of choices or directly to the specific Gene Page.
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• What is a Gene Page?
  All information in the dictyBase genomic database is organized from a "gene standpoint". The search for a gene will lead to a gene page that contains gene information, a discription, a summary, and, among other things, links to the sequence, a genome browser, literature, protein information, and a BLAST server.
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• How do I find Publications that are associated with a gene?
  If you are on a Gene Page you find a link to Literature for that gene in the colum on the right. There is a pull-down menue that by default is the "Literature Guide". Clicking on the "View" button returns a list of publications for the gene on the Gene Page.
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• Why should I Reserve a Gene Name?
  If you are working on a new gene which you have a named but not submitted to GenBank yet, you should reserve the name in dictyBase. This will show you if the name is still available, and prevent anyone else to use that name. To reserve a name, e-mail a curator who will create an "empty" Gene Page with a comment about the reservation in its "Locus History".
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• What is Curation?
  The data in dictyBase is under scientific curation to insure correct annotations. A dictyBase curator makes sure all genes have names and are associated with the correct gene products, gene ontology terms, and literature. Curators also write short gene summaries and curate the literature by assigning the papers to one or more literature topics. This curation results in an integration of the experimentally derived biological information with genomic data.
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• What is the chromosome 2 duplication?
  In strains AX3 and AX4 (the sequenced strain represented in dictyBase), chromosome 2 contains a duplication of approximately 750 kb. This duplication is not found in strain AX2. In the AX4 sequence represented in dictyBase, the region from base 2249563 to 3002134 is repeated between bases 3002337 and 375508. Electronic and manual annotations are made to genes on the first repeat of the duplication only. All Gene Pages of duplicated genes contain a note alerting the user to the fact that it is a duplicated gene, see carA and its duplicate DDB0217181. You can view lists of the genes present on the first repeat and on the second repeat.
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• What are the XXX in a BLASTP alignment?
  The stretch of 'XXX' appear in a BLASTP alignment because of a low complexity region in the protein sequence, which by default has been filtered. Filtering speeds up the BLAST search and is turned on by default. It can easily be turned off in the options on the BLAST page. Especially for very short proteins it is often useful to turn filtering off as otherwise hits might be missed. Note that when filtering is turned off it might take longer to get results.
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• What are BF, 2F, and 3F chromosomes?
  Those 'chromosomes' represent contigs that have not been anchored to a specific position on a real chromosome. Because the data model does not not allow 'floating' contigs, we concatenated these contigs into 'chromosomes' so that all sequences and their annotations could be presented. BF represents floating contigs that came from the Baylor Sequencing Senter (chromosomes 4, 5, and 6); 2F represents floating contigs that came specifically from the sequencing of chromosome 2, and 3F from chromosome 3. The inter-contig ordering in these chromosomes is meaningless, but the annotations are valuable nonetheless.
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