The following sections describe these new features in detail. From the ‘Report’ page the user may reformat, modify the current search and resubmit, or save the search strategy in My NCBI. After the search is submitted the ‘Job running’ page is shown until the search is done, after which the ‘Report’ page is shown. A user will normally enter through the ‘Home’ page and from there select a ‘BLAST form’ to submit a search. Each box represents a different page in the BLAST web application. Recent Results: links to unexpired BLAST results.īLAST screen flow map. Saved Strategies: filled-in BLAST forms that have been saved to My NCBI. Home: navigation to BLAST forms, organism-specific databases, specialized tools, tips and news. Each box in the figure represents a page in the BLAST web application. A page flow map of these steps is presented in Figure 2. The Recent Results page shows the status and some of the parameters of the user's unexpired BLAST jobs, and links directly to the BLAST Report for each job. From the Report, the user may now re-format the current job, run another BLAST job using the same parameters as a starting point, or navigate to one of the other application pages. When the job completes, BLAST presents the BLAST Report. The formatting parameters for a BLAST job may be changed on the Format Control page as the job runs, since formatting only occurs after search and alignment. When the user initiates a new job from a BLAST form, BLAST immediately presents the Job Running page, which reports the status of a running job and an estimate of how long it will take to complete. Also, in the header are tabs that provide access to the main application pages, as follows: Just below the header is a list of links (called ‘breadcrumbs’) that shows the current page's location and provides navigation to related pages, Figure 1. Each page has a header that contains links to the NCBI home page and a sign-in box for NCBI's login and customization interface, My NCBI. The key BLAST pages now have a consistent design and structure. The redesign replaces the old forms and navigation pages with an integrated web application that addresses all of these usability concerns. The legacy forms also did not take advantage of recent improvements in web technologies and improved browser support for web standards.
tblastx), and documentation was scattered and often out-of-date. Users had to remember the meaning of program names (e.g. sets of form parameters) could only be saved as browser bookmarks, tying them to a specific browser and machine. BLAST forms displayed a complex set of arcane input parameters that did not always correspond to the chosen program. The number of parameters made repeating searches error-prone. There was no way to get a list of recent searches, so when a browser window was closed, the search results were effectively lost. Form design was inconsistent and page navigation was difficult. The resulting gradual accretion of features caused a host of usability problems.
The legacy BLAST web interface grew incrementally as a group of web forms acting as a front-end to a growing collection of BLAST algorithms and programs.
The first phase of the redesign, on which we report here, defines consistent navigation between pages, offers new features such as the ability to save search parameter sets, and provides easy access to formatting controls, recent results and documentation. In addition to performing alignments, BLAST provides statistical information about an alignment this is the ‘expect’ value or false-positive rate.īLAST is one of the most widely used bioinformatics research tools, yet until recently, its web interface had numerous usability problems. BLAST is a heuristic that finds short matches between two sequences and attempts to start alignments from these ‘hot spots’. Several variants of BLAST compare all combinations of nucleotide or protein queries with nucleotide or protein databases. Basic Local Alignment Search Tool (BLAST) is a sequence similarity search program that can be used via a web interface or as a stand-alone tool to compare a user's query to a database of sequences ( 1, 2 ).
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