1 Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724
Making sequence data from genotyping assays available to the public in a web environment requires visualization tools for displaying alignments and polymorphism-related information.
We developed an interactive web-based viewer for displaying multiple sequence alignments. The viewer provides a set of features for assisting nucleotide polymorphism analysis. These include highlighting and providing statistics on positions of variation, displaying base-pair quality scores and a utility to filter out sequences of poor quality or low similarity to other sequences in the alignment. The viewer also provides general features such as search utilities and formatters for generating text dumps of sequences. Initially designed to support visualization needs of the maize diversity web site Panzea (www.panzea.org) and based on the Genomic Diversity and Phenotype Data Model (www.maizegenetics.net/gdpdm), viewer can be configured to retrieve sequence and related data from other sources with moderate or no additional coding.
The viewer is written in Perl and doesn't have demanding dependencies. Many of its features can be customized to fit individual web site needs through a simple configuration file. It provides a utility for pre-caching displays and allows faster response times for large alignment sets that would otherwise respond slowly.
The viewer is publicly available. Downloading information and a live installation can be accessed at the Panzea web site (www.panzea.org/db/snp_alignment/snp_cgi.dev.pl). Return to the Intl-PAG home page. For further assistance, e-mail help@www.intl-pag.org
Plant & Animal Genomes XIII Conference