Benchmarking Tools for the Alignment
of Functional Noncoding DNA

Pollard, Bergman, Stoye, Celniker & Eisen (2004) BMC Bioinformatics 5(1):6
View the figures from the paper
Download primary data
New tools and additional analysis
Enhanced with links
Find people involved in this project
Welcome to the web companion to our manuscript Benchmarking tools for the alignment of functional noncoding DNA (2004) BMC Bioinformatics. Download the PDF (580 Kb).
On this site you will find many features related to our analysis of pairwise genomic alignment tools:
View or download Figures from the paper.
Download primary Data from the paper.
Additional analysis and new alignment tools will be added to the Supplement section.
Find websites for alignment tools and our evolutionary simulation software in the Methods section.
Find and learn more about the People involved in this project.
November 21st 2005 - A new tool, ACANA, has been tested on our simulated data and performed quite well. Please visit for more details.

January 2005 - Thompson ISI has selected Benchmarking tools for the alignment of functional noncoding DNA as an Essential Science Indicator (ESI) "New Hot Paper." An interview with Casey Bergman about the manuscript can be found here.

July 22nd 2004 - A parsing error was discovered which affected the results presented in the original paper for the alignment tool BlastZ. We have corrected the error and have submited a correction for the paper to BMC Bioinformatics. While the major conclusions of the original paper remain the same, the quantitative results and some of the specific conclusions for BlastZ are different. All data and figures on this website now refer to the corrected BlastZ results.
This page was last updated on November 21st, 2005
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