Searching for evolutionary distant RNA homologs within large genomic sequences using partition function posterior probabilities

1. RNA-genome benchmark:

Full benchmark:

Query RNA without flanks: download
Query RNA with 50, 100, 150 nucleotide flanks: download

RFAM family alignments from which the benchmark was created

Training datasets: download

False positive datasets: download

README file

2. Software:

Probalign program with local alignment partition function matrices: download
Perl script to compute Probalign local alignments available here

3. Please contact Usman Roshan (usman@cs.njit.edu) for support.

Citation: U. Roshan, S. Chikkagoudar, and D. R. Livesay, Searching for evolutionary distant RNA homologs within large genomic sequences using partition function posterior probabilities, BMC Bioinformatics (In Press), 2008 (PDF)

Supplementary Material for the paper

Last updated Sept 24th, 2007