Efficient computation of optimal oligo-RNA binding.
We present an algorithm that calculates the optimal binding conformation and free energy of two RNA molecules, one or both oligomeric. This algorithm has applications to modeling DNA microarrays, RNA splice-site recognitions and other antisense problems. Although other recent algorithms perform the same calculation in time proportional to the sum of the lengths cubed, O((N1 + N2)3), our oligomer binding algorithm, called bindigo, scales as the product of the sequence lengths, O(N1*N2). The algorithm performs well in practice with the aid of a heuristic for large asymmetric loops. To demonstrate its speed and utility, we use bindigo to investigate the binding proclivities of U1 snRNA to mRNA donor splice sites.
Hodas
Nathan O
NO
Physics Department, Williams College, Williamstown, MA 01267, USA.
Aalberts
Daniel P
DP
D000465:Algorithms; D020029:Base Pairing; D001483:Base Sequence; D001665:Binding Sites; D019295:Computational Biology / Q000379:methods*; D009690:Nucleic Acid Conformation; D009843:Oligoribonucleotides / Q000737:chemistry* / Q000378:metabolism; D022821:RNA Splice Sites; D012333:RNA, Messenger / Q000737:chemistry / Q000378:metabolism; D012342:RNA, Small Nuclear / Q000737:chemistry / Q000378:metabolism; D016415:Sequence Alignment; D017423:Sequence Analysis, RNA / Q000379:methods*
D009843:Oligoribonucleotides; D022821:RNA Splice Sites; D012333:RNA, Messenger; D012342:RNA, Small Nuclear; C405483:U1 small nuclear RNA