NCBI BLAST: a better web interface

Abstract

Basic Local Alignment Search Tool (BLAST) is a sequence similarity search program. The public interface of BLAST, http://www.ncbi.nlm.nih.gov/blast, at the NCBI website has recently been reengineered to improve usability and performance. Key new features include simplified search forms, improved navigation, a list of recent BLAST results, saved search strategies and a documentation directory. Here, we describe the BLAST web application's new features, explain design decisions and outline plans for future improvement.

Figure 1.

Query sequence section of nucleotide blast form. The blue header provides links to the NCBI home page (left-most double helix) as well as tabs that can take a user to the BLAST home page, recent search results for a user, strategies saved via My NCBI and a help directory. On the far right is the My NCBI sign in box. Immediately below the header on the left side are bread-crumbs for navigation. The top part of the form is common to the major BLAST pages. As shown, this is followed by a form allowing the user to enter his/her query sequence and associated data. See text for details.

Figure 2.

BLAST screen flow map. Each box represents a different page in the BLAST web application. A user will normally enter through the ‘Home’ page and from there select a ‘BLAST form’ to submit a search. After the search is submitted the ‘Job running’ page is shown until the search is done, after which the ‘Report’ page is shown. From the ‘Report’ page the user may reformat, modify the current search and resubmit, or save the search strategy in My NCBI.

Figure 3.

Potential completions for organism names are suggested as the user types. The first 20 matches to the user's query are presented, with matches anywhere in the matching organism allowed (e.g. plat finds ‘duck billed platypus’ even though ‘plat’ is not at the beginning of the target text). See text for details.