BRAliBase (2.1)

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

• compalignp.tgz
• scif.tgz
• squid-1.9g.tar.gz

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MAFFT (ginsi) vs. ClustalW			MAFFT (ginsi) vs. Proalign
BRAliScore	SCI	Compalign	BRAliScore	SCI	Compalign
eps pdf png	eps pdf png	eps pdf png	eps pdf png	eps pdf png	eps pdf png
Muscle vs. ClustalW			Muscle vs. Proalign
BRAliScore	SCI	Compalign	BRAliScore	SCI	Compalign
eps pdf png	eps pdf png	eps pdf png	eps pdf png	eps pdf png	eps pdf png
PRRN vs. ClustalW			PRRN vs. Proalign
BRAliScore	SCI	Compalign	BRAliScore	SCI	Compalign
eps pdf png	eps pdf png	eps pdf png	eps pdf png	eps pdf png	eps pdf png

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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.

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Contact

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