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Even though in most of the cases analyzed, Geomfinder exhibited a better/similar performance when compared to other tools, it should be stressed that an exhaustive benchmarking was not intended, since our software executes a type of analysis that differs from those carried out by other available programs.
To further assess the validity of the sieving method we have performed an exhaustive benchmarking against the SISYPHUS database, which contains a set of 149 manually curated MSAs classified into 3 categories [8].
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Other than being an invaluable source of information, we suggest this data could be used also to build exhaustive benchmark sets for motif discovery algorithms.
The NRLiSt is an exhaustive, NR-focused, benchmarking database.
We begin by validating and benchmarking the WL method against the exhaustive method RNAsubopt Wuchty et al. (1999), that enumerates all secondary structures of a given RNA sequence.
Ask for Benchmarking.
"We've been benchmarking them.
The first exhaustive protein alignment benchmark [ 10] used the so called BAliBASE (Benchmark Alignment dataBASE) [ 11].
Using a reference standard data set and an exhaustive search algorithm for benchmarking, we show that the cost function plays the most significant role in realizing high levels of performance.
National benchmarks also tumbled.
Moreover, the performance upper bound "Optimal" is obtained by using the exhaustive search as a benchmark.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com