Jump to gene
Welcome to the "How To" Page of CryptoBase!
This page provides instructions on how to use the database to explore the C. neoformans serotype A genome database. In addition, it provides some general information about CryptoBase. There are three types of pages of particular utility. The "Search Page" allows users to identify genes based on a large variety of powerful criteria. The "Results Pages" displays the results of searches in graphical form. "Gene Pages" describe individual genes.
The Search page allows users to find a set of genes by building a query based on a number of criteria. Users will immediately notice that there are two halves of the Search Page, one for creating a search for the genes you would like to see and one for creating a search for the genes you do not wish to see in the results (that is criteria for "inclusion" on the left half of the page and criteria for "exclusion" on the right half of the page).
The Search Results pages display the C. neoformans genes that adhere to the search criteria given to the database by users. The pages list an internal called CDSid, the Name of the gene and a proposed description. It also shows an image generated by SMART of protein motifs of each gene returned by the search. By clicking on the CDSid link, users are taken to the Gene Prediction page for that particular gene. An example of a Search Results Page is shown below.
Gene Prediction page
At the top of the Gene Prediction page is the name of the predicted ORF, followed by a snapshot view of its region in the genome. Below that is some general information about the gene including the proposed name and description, the homology to other organisms and the results from the SMART analysis. The BLAST hits against the nonredundant protein database are next. At the bottom is some information about the coding sequence and protein sequence for the gene as well as the microarray oligonucleotide generated for it.
Gene Naming conventions
Genes with a hit to a gene in S. cerevisiae are given an equivalent name. If multiple genes have the same S. cerevisiae gene as its best hit, 100 is added to the number of S. cerevisiae gene and the C. neoformans homologs are named sequentially. C. neoformans genes without a S. cerevisiae hit are given the standard CN# designation from the serotype D homolog assigned by TIGR and Stanford. C. neoformans genes described in the literature are named based on the first refereed literature citation. We propose that naming conflicts are resolved by the groups involved and that the webmaster be informed when a consensus is reached by those involved.
Database Feature Improvements
Please e-mail the webmaster for suggestions for feature improvements for the database. These will be discussed internally and those features deemed useful and implementable will be added.