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 v1.4 program with local alignment partition function matrices: download
Perl scripts to compute Probalign local alignments: cover.pl and probalign_multiple_hits.pl. Please see this README for instructions.

3. Additional materials

Perl scripts used in the experimental study available here (README)
Files containing experimental results outputted by scripts available here

4. PLAST-ncRNA webserver: Partition function Local Alignment Search Tool for non-coding RNA sequences.

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

Citation: U. Roshan (corresponding author), S. Chikkagoudar, and D. R. Livesay, Searching for RNA homologs within large genomic sequences using partition function posterior probabilities, BMC Bioinformatics, 9:61, 2008 (PDF)

Supplementary Material for the paper

Last updated Mar 30th, 2010