ArticleNucleic acids research2004
Predicting genes expressed via -1 and +1 frameshifts.
Article in Nucleic acids research, 2004. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 papers.
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Who cites it
30 citing papers in PubMed.
- Programmable modulation of ribosomal frameshifting by mRNA targeting CRISPR-Cas12a system.iScience · 2023Article
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- RNA-mediated translation regulation in viral genomes: computational advances in the recognition of sequences and structures.Briefings in bioinformatics · 2020Review
- Isolation and characterisation of novel phages infecting Lactobacillus plantarum and proposal of a new genus, "Silenusvirus".Scientific reports · 2020Article
- Functional and Evolutionary Characterization of a Gene Transfer Agent's Multilocus "Genome".Molecular biology and evolution · 2016Article
- Two Novel Relative Double-Stranded RNA Mycoviruses Infecting Fusarium poae Strain SX63.International journal of molecular sciences · 2016Article
- Human DNA tumor viruses generate alternative reading frame proteins through repeat sequence recoding.Proceedings of the National Academy of Sciences of the United States of America · 2014Article
- Yeast telomere maintenance is globally controlled by programmed ribosomal frameshifting and the nonsense-mediated mRNA decay pathway.Translation (Austin, Tex.) · 2013Article
- Article
- Adaptive immunity restricts replication of novel murine astroviruses.Journal of virology · 2012Article
- Comparative analysis of two phenotypically-similar but genomically-distinct Burkholderia cenocepacia-specific bacteriophages.BMC genomics · 2012Article
- Control of gene expression by translational recoding.Advances in protein chemistry and structural biology · 2012Review
- Endogenous ribosomal frameshift signals operate as mRNA destabilizing elements through at least two molecular pathways in yeast.Nucleic acids research · 2011Article
- Short- and long-term evolutionary dynamics of bacterial insertion sequences: insights from Wolbachia endosymbionts.Genome biology and evolution · 2011Article
- Mining Functional Elements in Messenger RNAs: Overview, Challenges, and Perspectives.Frontiers in plant science · 2011Article
- Identification of the main promoter directing cereulide biosynthesis in emetic Bacillus cereus and its application for real-time monitoring of ces gene expression in foods.Applied and environmental microbiology · 2010Article
- Recode-2: new design, new search tools, and many more genes.Nucleic acids research · 2010Article
- FSscan: a mechanism-based program to identify +1 ribosomal frameshift hotspots.Nucleic acids research · 2009Article
- Identification of a tail assembly gene cluster from deep-sea thermophilic bacteriophage GVE2.Virus genes · 2009Article
- Complete genome sequence of a highly divergent astrovirus isolated from a child with acute diarrhea.Virology journal · 2008Article
Corrections and comments
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
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/.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.