GeneDB

Database Analysis

1. What database did you access? (link to the home page of the database)
   • We accessed Gene DB Gene DB.
2. What is the purpose of the database?’’
   • The purpose of Gene DB, is to provide the public with reliably sequenced genomes as soon as they become available. Gene DB offers the sequences of a variety of different organisms in the pathogenic group.
3. What biological information does it contain?
   • Since Gene DB is concerned with pathogens, it includes information on the disease that each species is responsible for creating in different organisms. The database contains the seqeunces data of each pathogen as well and it includes articles relating to that specific organism. Descriptives of each pathogen consist of:
     1. protein length
        • maximum length
        • minimum length
     2. molecular mass
        • minimum mass
        • maximum mass
     3. gene type
        • protein-coding
        • pseudogene
        • rRNA
        • snoRNA
        • snRNA
        • tRNA
        • miscRNA
     4. date sequenced was last modified
     5. location
        • region
        • boundaries
     6. protein targeting
        • signal peptide
        • GPI anchor
        • Apicoplast
     7. transmembrane helices
        • minimum number of domains
        • maximum number of domains
4. What species are covered in the database?
   • Gene DB covers various species of bacteria (e.g. Apicomplexan and Plasmodium)
5. What biological questions can it be used to answer?
   • GeneDB can answer numerous questions about sequenced genomes of pathogens. Any off the above descriptives can be search for specifically among all the genomes present on the database.
6. What type (or types) of database is it (sequence, structure model organism, or specialty [what?]; primary or “meta”; curated electronically, manually [in-house], manually [community])?
   • GeneDB is concerned with the sequenced genomes of different pathogens. The database is curated electronically in a community setting.
7. What individual or organization maintains the database?
   • The Sanger Institute appears to run the website, but the sequences are a product of the Pathogen Group.