PARTS
updated 3/27/2008
PARTS is a computer algorithm that improves the accuracy of structure prediction by combining free energy minimization and comparative sequence analysis to find a secondary structure common to two sequences. It uses a pseudo-free energy change score that depends on single sequence base pairing probabilities for each sequence and alignment probabilities calculated using a Hidden Markov Model. The maximum posterior probability output is both a maximally scoring common secondary structure for each sequence and a sequence alignment determined by structure comparison. Furthermore, the probabilities for each base pair in the common secondary structure is determined using a partition function.
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Download PARTS
Download is available in a gzipped tar file format.
PARTS is fully described in:
Harmanci, A. O., Sharma, G., & Mathews, D. H. (2008). PARTS: Probabilistic Alignment for RNA joinT Secondary structure prediction. Nucleic Acids Research. In Press.
