An accelerated algorithm for calculating the secondary structure of single stranded RNAs

Eliahu Comay, Ruth Nussinov, Oded Comay

Research output: Contribution to journalArticlepeer-review

Abstract

We describe a code designed for secondary structure computation of single stranded RNA molecules. While it incorporates the same principles as the original algorithm of Nussinov et al (1978), its restructuring improves the logic and the approach of the codes based on it. For long sequences the code is at least an order of magnitude faster. For a chain n nucleotides long, references to computer disk memory are reduced from n3 to less than n2. For n»100, disk references behave like n3/6000.

Original languageEnglish
Pages (from-to)53-66
Number of pages14
JournalNucleic Acids Research
Volume12
Issue number1 PART1
DOIs
StatePublished - 11 Jan 1984
Externally publishedYes

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