Research article
Towards realistic benchmarks for multiple alignments of non-coding sequences
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* Corresponding author: Saurabh Sinha sinhas@illinois.edu
1 Department of Computer Science, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
2 Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
BMC Bioinformatics 2010, 11:54 doi:10.1186/1471-2105-11-54
Published: 26 January 2010Additional files
Additional file 1:
Performance of multiple alignment tools compared by alignment sensitivity. The scores were calculated by using all synthetic data sets (left panel), and by using only data sets where the expected number of insertions is two times more than the number of deletions or vice versa (middle and right panels respectively).
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Additional file 2:
Performance of multiple alignment tools compared by alignment specificity. The scores were calculated by using all synthetic data sets (left panel), and by using only data sets where the expected number of insertions is two times more than the number of deletions or vice versa (middle and right panels respectively).
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Additional file 3:
An example data set from the benchmark shown (in part) with true alignment (top panel) and alignments computed by each different programs.
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Additional file 4:
Dependence of performance (sensitivity (left) and specificity (right)) of each alignment program on various descriptive statistics of the data sets.
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Additional file 5:
Performance of multiple alignment tools compared by alignment sensitivity of pairs of species. The scores were calculated by using all synthetic data sets (left panel), and by using only data sets where the expected number of insertions is two times more than the number of deletions or vice versa (middle and right panels respectively).
Format: DOC Size: 191KB Download file
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Additional file 6:
Performance of multiple alignment tools compared by alignment specificity of pairs of species. The scores were calculated by using all synthetic data sets (left panel), and by using only data sets where the expected number of insertions is two times more than the number of deletions or vice versa (middle and right panels respectively).
Format: DOC Size: 195KB Download file
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Additional file 7:
Comparison of estimated alignment sensitivity and specificity, using Mlagan or Pecan, as obtained from the Pollard et al. [21] benchmark and from our benchmark.
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Additional file 8:
Comparison of estimated alignment sensitivity and specificity as obtained from the Pollard et al. benchmark.
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Additional file 9:
Phylogenetic trees and branch lengths in Newick format.
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Additional file 10:
Genome-wide distribution of the fraction of conserved blocks estimated by using Phastcons conservation scores and multiple alignments of Drosophila non-coding sequences obtained from UCSC Genome Browser Database.
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Additional file 11:
Descriptive statistics of traditional and new benchmarks.
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