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ARS Home » Northeast Area » Ithaca, New York » Robert W. Holley Center for Agriculture & Health » Plant, Soil and Nutrition Research » Research » Publications at this Location » Publication #206544

Title: Look-Align: an interactive web-based multiple sequence alignment viewer with polymorphism analysis support

item Ware, Doreen

Submitted to: Bioinformatics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 1/26/2007
Publication Date: 2/28/2007
Citation: Canaran, P., Stein, L., Ware, D. 2007. Look-Align: an interactive web-based multiple sequence alignment viewer with polymorphism analysis support. Bioinformatics. 22(7):885-886.

Interpretive Summary: Variations in the genome of an organisms across different samples, allow scientists to study regions of interest in the genome (e.g. regions responsible for resistance or susceptibility to diseases in maize). The scientists choose a particular region in the genome of the organism in question and sequence it from a number of samples. For each sample, they obtain the DNA sequence of the region, which consists of a series of four letters, A, T, C and G, each representing a different type of chemical that make up the DNA sequence. The scientists overlap these sequences of letters using computer software to generate a "multiple sequence alignment." A multiple sequence alignment describes the matching and non-matching (polymorphic) points in the studied region of the genome. These variation points are then further processed. We developed an application, Look-Align, that allows the scientists to make their multiple sequence alignments available on the web to the scientific community. The software provides a number of features that help the scientists with their analysis. For example, the user can interactively apply filters on the views, navigate along the multiple sequence alignment and see results of specific calculations. The software is built using "open source" software components, which allows it to be freely used by other groups. In addition, it is designed as a generic tool, which supports a high level of customization. This allows it to be used by other groups, even if their data infrastructure is different than our project web site, Panzea ( We have documented and packaged the software and made it available to the scientific community through our project website (

Technical Abstract: We have developed Look-Align, an interactive web-based viewer to display pre-computed multiple sequence alignments. Although initially developed to support the visualization needs of the maize diversity website Panzea (, the viewer is a generic stand-alone tool that can be easily integrated into other websites.