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Data provide to benchmark a method

The current verion of BRASERO contains 5 benchamrks, for 5 RNA families.

See Benchmarking protocol for details on the structure of a benchmarking data set.

Noise sources

To generate sequences of set F, we use various sources:

  • random genome segments from viral genomes
  • random genome segments from encode sequence (hg18_dna range=chr5:131284314-132284313)
  • GenRGenS: a generator of random sequences or structures

Adding new RNA families

This is a short how-to explaining how we generated data sets for each family.

The R set

First we looked for 6 representants of each family, carefully chosen to be as representative as possible (i.e. sequence/structure are not very close within a family).

The T set

Then we selected a hundred sequences of RNA known to belong to the family.

The T2 set

To fold each sequence of the set T we used a python script With our sequences in stored in distinct files, we did fold them as follows:

for i in *.fasta
do --mfold  --mfold-opt " P=10 W=10 MAX=5 " \
              -d "TRUE %f: %s => %e (%x) % %m %o %N" -f ../true_events.srp.dp $i

In this example, only mfold is used to fold the sequence but rnashapes and rnasubopt are also available. Please use -h to obtain information on how to use this script.

Note: the mfold parameter depends on the input

The F2 set:

We directly build the set F2 from the noise source (encode or viral genome) using the script. First extracted the lengths of each reference structure (for example 120,121,140,90,120,130).

If the noise source (sequence) is in a file named noise.fasta and we want to generate noise in the file noise.dp, we use the following command: --mfold  --mfold-opt " P=10 W=10 MAX=5 " -d "%f: %s => %e (%x) % %m %o %N" -f noise.dp \
 --sequence-name noise.fasta noise.fasta  {::50}/90,{::100}/120,{::50}/121,{::50}/130,{::50}/140

This line tell to use noise.fasta as input and randomly choose 50 sequences of length 90, 100 of length 120, 50 of length 121, ... (see -h for a description of the parameters) This give 300 sequences for F (the size of F2 depends on the folders options).

Note: again, the mfold parameter depends on the input

Assembling the data together

Finally, we created two files for each benchmark: the first usually called reference_set contains the paths to references structures and the second, true_events_with_noise, contains the paths to T2 and F2 structures files.

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Page last modified on December 09, 2010, at 03:17 PM EST