BRAliBase (2.1)


About BRAliBase

The term BRAliBase was coined back in 2004 at the "Computational roads to the RNA world workshop" at Bielefeld University.
The idea was to establish an RNA counterpart of the protein specific "Benchmark Alignment Database" .
BRAliBase became more than just a collection of alignments. The BRAliBase homepage (BRAliBase I, BRAliBase II) is hosted by Paul Gardner .

Here you will find Supplementary Data for BRAliBase 2.1 as published in:
Wilm, A., Mainz, I. & Steger, G. (2006).
An enhanced RNA alignment benchmark for sequence alignment programs.
Algorithms Mol. Biol. 1, 19.


This is a sequel to BRaliBase II: Gardner PP, Wilm A & Washietl S (2005).

Programs Used For Scoring


Reference Alignments


Score Files


APSI vs. Score Plots for all Programs in Table 5

k2 k3 k5
BRAliScore SCI Compalign BRAliScore SCI Compalign BRAliScore SCI Compalign
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k7 k10 k15
BRAliScore SCI Compalign BRAliScore SCI Compalign BRAliScore SCI Compalign
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Ranktest Results (Table 5)


"Effect of Sequence Number on Performance"
aka.
"Iterative vs. Purely Progressive Programs"

MAFFT (ginsi) vs. ClustalW MAFFT (ginsi) vs. Proalign
BRAliScoreSCICompalign BRAliScoreSCICompalign
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Muscle vs. ClustalW Muscle vs. Proalign
BRAliScoreSCICompalign BRAliScoreSCICompalign
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PRRN vs. ClustalW PRRN vs. Proalign
BRAliScoreSCICompalign BRAliScoreSCICompalign
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Comparison of CPU times

The table summarizes (for each of the programs from Table 5) the mean user time (in s) necessary to calculate a single alignment. Be extremely careful with the given numbers.

Program Mean time
ClustalW 0.07
MAFFT 0.10
MUSCLE 0.05
PCMA 0.18
POA 0.04
ProAlign 4.77
ProbConsRNA 0.41
Prrn 0.14

Contact

If you find bugs, need help, want to discuss results, don't hesitate to contact
Gerhard Steger