posted this on August 15, 2012 11:27 AM
The search feature available on the left-hand portion of the home page (Figure 1) is designed to simplify the search process for many commonly asked queries by immunologists. It allows greater control in the search than available in the keyword search and is less involved than the Advanced queries. The user specifies the epitope structure with radio button selections for Any, Linear Peptide, Discontinuous Peptide, and Non-Peptidic. The user can prescribe a linear peptide sequence and the type of search to be performed on it. When specifying a linear sequence, a window appears in which the user must enter the sequence and press "Apply". The user can prescribe the type of search desired - an exact match to the entered sequence, a substring search where epitopes are found that contain the sequence within its overall structure, or a homologous peptides at sequence at identity levels of 70%, 80%, or 90% as determined by BLAST. The user can specify a non-peptidic structure with the Molecule Finder.
Figure 1. Home page Simple Search
In addition to finding peptides in the database that contain the specified amino acid sequence, the linear peptide substring search finds epitopes within the input sequence itself. For example, when the sequence AELLVALENQHTIDL is submitted for a substring search, the query results, shown in Figure 2, yields five peptide sequences. Three of them (the second, third, and fifth) contain the input sequence. The two others (the first and fourth) are substrings of the input sequence that are also epitopes contained in the IEDB.
Figure 2. Query results for a substring search performed on the input sequence AELLVALENQHTIDL
An autocomplete feature is available for the Molecule, Organism, and Allele Finders. For example, as one types “hem” in the Source Antigen field in the Epitope Source section, several choices start to appear in a list below the text field, including “hemolysin”, “hemK protein”, and “hemagglutinin”. The user can click on a selection from the list or can continue typing to further narrow down choices. Likewise, a user may type “human” or “homo” to select “homo sapiens” in the Host Organism field. The list of matches includes scientific names and synonyms. These actions enable users to quickly specify their search parameters without using the finders. The autocomplete applies wherever the input field has “Enter Search” in grey. Use of the autocomplete circumvents the need to use the finders.
If the user decides not to use the autocomplete feature for a search field, they will need to use the finders. The epitope source can be prescribed for the source organism and source antigen by using the organism finder and molecule finder, respectively. The molecule finder for the epitope source is again different from the non-peptidic molecule mentioned above and the molecule finders available on the Advanced Query papges. This finder has tree structures for non-peptidic molecules and peptidic molecules, as described in Home Page Molecule Finder tutorial. The user can decide whether to include B cell responses, T cell responses, MHC binding, and/or MHC ligand elution results in the search (at least one must be checked). The host organism, the MHC restriction, and the MHC class can also be specified with the help of the organism finder and the allele finder. The fields using finders will allow multiple selections as search criteria. In these cases the selections are treated as a set. Records will be considered a match if they include at least one of the selected values in the set. The search is executed by selecting the Search button and query results can be viewed on the Search Result Summary page.
A new feature introduced in 2011 is the Immune Mediated Disease Association search that was added as an experimental feature on the IEDB home page search and in the Advanced Search pages. It is available on the home page search interface between the Epitope Source and the Immune Recognition Context field partitions. The Disease Finder in described in the Using the Disease Finder tutorial.
Finally, a link to “Help with Common Queries” is located at the bottom of the Search panel. This links to a series of 16 questions that have been useful in preparing the epitope meta-analyses conducted and published by LIAI. More information about the Common Queries is available in Queries and Reporting forum.