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Search Functions The main search function of the database is provided through four pull-down menus (Figure 1). The default option in the top menu is to select all proteins in the database. Users may type any part of a protein name in the text field next to "Protein Name Contains" and then click "check" button. A list of proteins with names matching the typed text will be displayed in the pull-down menu (If the "check" button is clicked without any text typed, a list of all proteins will be displayed). Users may then select one or more proteins from the list. Holding "Ctrl" key to select multiple choices (Figure 2).   The bottom three pull-down menus are devoted to polyanions, source species of PABPs, and the methods used to determine the PA-PABP interactions. Multiple choices can be made in all these menus via holding "Ctrl" key (Figure 2). Polyanion menu supports "OR" (bind to one or more selected polyanions) and "AND" (bind to all selected polyanions) Boolean operations. Species and method only use "OR" operation.   Search Results After choices are made in all four menus (the default option considers all choices), users may click "search" button to retrieve results that match all search options (Figure 3a, 3b). The results are displayed in a table. Clicking Links in protein and reference columns open another window displaying additional information available in the database. Links to NCBI or PubMed are available in the new window. Users may generate a protein sequence file in FASTA format via clicking the link on the top of the search result page. Users of IE need to save the FASTA file and then open it using any text processing programs (such as notepad or WordPad). Utilities Four different searches are also available for other common tasks (Figure 4).  1. Search by author's name Typing any part of an author' name and then clicking "search by author's name" button results in a table of relevant papers. The last column in the table has the links to the PABPs reported in the papers (Figure 5). Notes: author information is retrieved from PubMed. First names of the authors may not be available.  2. Commonality matrix Commonality matrix is an N x N matrix, where N is the number of polyanions having entries in the database (Figure 6). Each element in the matrix gives the total number of proteins that have been identified to interact with polyanions on that row and that column of the matrix; clicking this number will produce a report listing all those proteins.  3. List proteins by number of hits This list is a summary of all proteins in the database. Columns of protein id, protein name, species, number of polyanions interacting with the protein are sortable. This list is useful when users need to identify proteins that interact with multiple polyanions (Figure 7).  4. List all proteins in the publicly available database This option lists all proteins in the database with links to NCBI protein database. |
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Construction crew : Jianwen Fang, Yinghua Dong, Nazila Salamat-Miller, Russell Middaugh. |
| Copyright ©2007 |