How to search the database

Search Dialog

The search dialog allows to search ProSAS for Ensembl gene or Ensembl transcript ids, Gene descriptions, Uniprot gene names, Genes matching patterns, Swissprot/Uniprot identifiers or Affymetrix probeset ids. Queries match an identifier if they are a substring of the corresponding identifier, i.e. ENSG matches all human genes in the database. The results of your query will be opened in a new tab such that you can easily keep track of several queries if you like.

To restrict your query to database entries that are modelled by protein structure, please check the Require structure annotation checkbox. To further specify the required quality of the structure models, you can use the sequence identity and the coverage thresholds. For example a threshold of 40% sequence identity and 75% coverage will only select entries that can be modelled by protein structures from the PDB with a sequence identity of more than 40% between transcript and PDB structure. Additionally, the structure has to cover more than 75% of the database entry.

To search the database please execute the following steps:

  • Select the type of identifier you want to search for from the drop down list.
  • Check the Require structure annotation checkbox if you want to restrict your search to proteins with modelled structure. Specify the sequence identity and coverage thresholds if you like.
  • Type your query in the query text field and click the Search button or press Enter
  • The results of your search will be opened in a new tab of the ProSAS application (see Search Result documentation)

Search Results

This panel lists all the results for your query in a new tab of the ProSAS application. This way you can easily keep track of different queries at a time which are listed in different tabs. By default twenty results are shown per result page. If you want to see more results per page, change the value in the drop down menue "Results per page". At the bottom of the list you can browse through all the results that are available. To see the details of a specific query result click on it. This will open a new tab in the application showing details for genes or transcripts associated with the corresponding result. If you want to save the genes resulting from your search, click on the Save selected Gene Data button.