Predicting genes expressed via -1 and +1 frameshifts.
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 approximately 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/.
Moon
Sanghoon
S
School of Computer Science and Engineering, Inha University, Inchon 402-751, Korea.
Byun
Yanga
Y
Kim
Hong-Jin
HJ
Jeong
Sunjoo
S
Han
Kyungsook
K
D000465:Algorithms; D019295:Computational Biology / Q000379:methods*; D018965:Frameshifting, Ribosomal; D016680:Genome, Bacterial; D020407:Internet; D016366:Open Reading Frames; D010454:Peptide Termination Factors / Q000235:genetics; D011506:Proteins / Q000235:genetics; D012333:RNA, Messenger / Q000737:chemistry; D012984:Software
D010454:Peptide Termination Factors; D011506:Proteins; D012333:RNA, Messenger; C031017:ornithine decarboxylase antizyme; C041460:peptide chain termination release factor 2