title: PKscan: a program to identify H-type RNA pseudoknots in any RNA sequence with unlimited length.
abstract: A computer program written in C++ has been developed which can detect all potential H-type RNA pseudoknots within any given RNA sequence. There is no limit on the length of the input sequence. A validation run of the program using the full-length (8173 nt) genomic mRNA of simian retrovirus type-1 (SRV-1) identifies the established -1 frameshift stimulating pseudokont at the gagpro junction as the most stable pseudoknot within the genomic mRNA.
authors.affiliation: Department of Computer Science, Southern Illinois University at Carbondale, IL 62901, USA.
authors.forename: Xiaolan
authors.initials: X
authors.lastname: Huang
authors.forename: Zhihua
authors.initials: Z
authors.lastname: Du
authors.forename: Jie
authors.initials: J
authors.lastname: Cheng
authors.forename: Qiang
authors.initials: Q
authors.lastname: Cheng
keywords: -1 ribosomal frameshifting; RNA; computational biology; pseudoknot