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Nucleic Acids Research 2004 32(16):4884-4892; doi:10.1093/nar/gkh829
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Published online 15 September 2004

Nucleic Acids Research, Vol. 32 No. 16 © Oxford University Press 2004; all rights reserved

Predicting genes expressed via –1 and +1 frameshifts

Sanghoon Moon, Yanga Byun, Hong-Jin Kim1, Sunjoo Jeong2 and Kyungsook Han*

School of Computer Science and Engineering, Inha University, Inchon 402-751, Korea, 1 College of Pharmacy, Chung-Ang University, Seoul 156-756, Korea and 2 Department of Molecular Biology, Dankook University, Seoul 140-714, Korea

* To whom correspondence should be addressed. Tel: +82 32 860 7388; Fax: +82 32 863 4386; Email: khan{at}inha.ac.kr

Received August 8, 2004; Accepted August 27, 2004

Computational identification of ribosomal frameshift sites in genomic sequences is difficult due to their diverse nature, yet it provides useful information for understanding the underlying mechanisms and discovering new genes. We have developed an algorithm that searches entire genomic or mRNA sequences for frameshifting sites, and implements the algorithm as a web-based program called FSFinder (Frameshift Signal Finder). The current version of FSFinder is capable of finding –1 frameshift sites on heptamer sequences X XXY YYZ, and +1 frameshift sites for two genes: protein chain release factor B (prfB) and ornithine decarboxylase antizyme (oaz). We tested FSFinder on ~190 genomic and partial DNA sequences from a number of organisms and found that it predicted frameshift sites efficiently and with greater sensitivity and specificity than existing approaches. It has improved sensitivity because it considers many known components of a frameshifting cassette and searches these components on both + and – strands, and its specificity is increased because it focuses on overlapping regions of open reading frames and prioritizes candidate frameshift sites. FSFinder is useful for discovering unknown genes that utilize alternative decoding, as well as for analyzing frameshift sites. It is freely accessible at http://wilab.inha.ac.kr/FSFinder/.


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