Benchmarking Tools for the Alignment
of Functional Noncoding DNA

Pollard, Bergman, Stoye, Celniker & Eisen (2004) BMC Bioinformatics 5(1):6
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Data, Results and Code from the paper are available for download in tar archive format. We have provided a brief description of the file names and formats within each archive. Please contact us if you need additional explanation or data.
Results in Figures 1 through 6:
Figure 1 - Noncoding Sequence Lengths - [figure1.tar.gz (85Kb)]
Figure 2 - Simulation Statistics - [figure2.tar.gz (3.4Kb)]
Figure 3 - Overall Coverage - [figure3.tar.gz (4.4Kb)]
Figure 4 - Overall Sensitivity - [figure4.tar.gz (5.8Kb)]
Figure 5 A & B - Constraint Coverage - [figure5AB.tar.gz (2.8Kb)]
Figure 5 C & D - Constraint Sensitivity - [figure5CD.tar.gz (3.6Kb)]
Figure 6 A & B - Constraint Specificity - [figure6AB.tar.gz (3.5Kb)]
Figure 6 C & D - Local Constraint Sensitivity - [figure6CD.tar.gz (3.5Kb)]
Simulated Alignments & Associated Files:
Without Constraint & Without Indels - [sim.0.0.0000.tar.gz (129Mb)]
Without Constraint & With Indels - [sim.0.0.0005.tar.gz (150Mb)]
With Constraint & Without Indels - [sim.0.2.0.0000.tar.gz (163Mb)]
With Constraint & With Indels - [sim.0.2.0.0005.tar.gz (196Mb)]
Avid Alignments:
Without Constraint & Without Indels - [avid.0.0.0000.tar.gz (588Mb)]
Without Constraint & With Indels - [avid.0.0.0005.tar.gz (598Mb)]
With Constraint & Without Indels - [avid.0.2.0.0000.tar.gz (566Mb)]
With Constraint & With Indels - [avid.0.2.0.0005.tar.gz (613Mb)]
BlastZ Alignments:
Without Constraint & Without Indels - [blastz.0.0.0000.tar.gz (2.4Mb)]
Without Constraint & With Indels - [blastz.0.0.0005.tar.gz (5.9Mb)]
With Constraint & Without Indels - [blastz.0.2.0.0000.tar.gz (14Mb)]
With Constraint & With Indels - [blastz.0.2.0.0005.tar.gz (20Mb)]
BlastZ-A Alignments (Author Recommended Parameter Settings):
Without Constraint & Without Indels - [blauthorstz.0.0.0000.tar.gz (2.6Mb)]
Without Constraint & With Indels - [blauthorstz.0.0.0005.tar.gz (6Mb)]
With Constraint & Without Indels - [blauthorstz.0.2.0.0000.tar.gz (15Mb)]
With Constraint & With Indels - [blauthorstz.0.2.0.0005.tar.gz (22Mb)]
Chaos Alignments:
Without Constraint & Without Indels - [chaos.0.0.0000.tar.gz (1Mb)]
Without Constraint & With Indels - [chaos.0.0.0005.tar.gz (0.9Mb)]
With Constraint & Without Indels - [chaos.0.2.0.0000.tar.gz (2.9Mb)]
With Constraint & With Indels - [chaos.0.2.0.0005.tar.gz (3.2Mb)]
Chaos-A Alignments (Author Recommended Parameter Settings):
Without Constraint & Without Indels - [chauthoros.0.0.0000.tar.gz (2Mb)]
Without Constraint & With Indels - [chauthoros.0.0.0005.tar.gz (3.9Mb)]
With Constraint & Without Indels - [chauthoros.0.2.0.0000.tar.gz (3.8Mb)]
With Constraint & With Indels - [chauthoros.0.2.0.0005.tar.gz (7.7Mb)]
ClustalW Alignments:
Without Constraint & Without Indels - [clustalw.0.0.0000.tar.gz (70Mb)]
Without Constraint & With Indels - [clustalw.0.0.0005.tar.gz (73Mb)]
With Constraint & Without Indels - [clustalw.0.2.0.0000.tar.gz (68Mb)]
With Constraint & With Indels - [clustalw.0.2.0.0005.tar.gz (74Mb)]
DiAlign Alignments:
Without Constraint & Without Indels - [dialign.0.0.0000.tar.gz (75Mb)]
Without Constraint & With Indels - [dialign.0.0.0005.tar.gz (76Mb)]
With Constraint & Without Indels - [dialign.0.2.0.0000.tar.gz (73Mb)]
With Constraint & With Indels - [dialign.0.2.0.0005.tar.gz (77Mb)]
Lagan Alignments:
Without Constraint & Without Indels - [lagan.0.0.0000.tar.gz (70Mb)]
Without Constraint & With Indels - [lagan.0.0.0005.tar.gz (74Mb)]
With Constraint & Without Indels - [lagan.0.2.0.0000.tar.gz (69Mb)]
With Constraint & With Indels - [lagan.0.2.0.0005.tar.gz (75Mb)]
Needle (Emboss's Needleman-Wunsch) Alignments:
Without Constraint & Without Indels - [needle.0.0.0000.tar.gz (166Mb)]
Without Constraint & With Indels - [needle.0.0.0005.tar.gz (172Mb)]
With Constraint & Without Indels - [needle.0.2.0.0000.tar.gz (157Mb)]
With Constraint & With Indels - [needle.0.2.0.0005.tar.gz (171Mb)]
Waba Alignments:
Without Constraint & Without Indels - [waba.0.0.0000.tar.gz (14Mb)]
Without Constraint & With Indels - [waba.0.0.0005.tar.gz (9.9Mb)]
With Constraint & Without Indels - [waba.0.2.0.0000.tar.gz (55Mb)]
With Constraint & With Indels - [waba.0.2.0.0005.tar.gz (57Mb)]
Code:
Scripts for calculating performance measures - [scripts.tar (20Kb)]
This page was last updated on November 26th, 2004
Problems with the website? Please contact dpollard@socrates.berkeley.edu.