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Prediction of Ribosomal -1 Frameshifts in the Escherichia coli K12 Genome

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Prediction of Ribosomal -1 Frameshifts in the Escherichia coli K12 Genome

Auteurs : Sanghoon Moon [Corée du Sud, Niger] ; Yanga Byun [Corée du Sud, Niger] ; Kyungsook Han [Corée du Sud]

Source :

Lecture Notes in Computer Science [ 0302-9743 ]

RBID : ISTEX:24886CA60B13DC91125D83598620974163B8C6B3

Abstract

Abstract: Ribosomal frameshifting at a particular site can yield two protein products from one coding sequence or one protein product from two overlapping open reading frames. Many organisms are known to utilize ribosomal frameshifting to express a minority of genes. However, finding ribosomal frameshift sites by a computational method is difficult because frameshift signals are diverse and dependent on the organisms and environments. There are few computer programs available for public use to identify frameshift sites from genomic sequences. We have developed a web-based application program called FSFinder2 for predicting frameshift sites of general type. We tested FSFinder2 on the Escherichia coli K12 genome to detect potential -1 frameshifting genes. From the genome sequence, we identified 18,401 frameshift sites following the X XXY YYZ motif. 11,530 frameshift sites out of the 18,401 sites include secondary structures. Comparison with the GenBank annotation produced 11 potential frameshift sites, including 3 known frameshift sites. The program is useful for analyzing frameshifts of various types and for discovering new genes expressed by frameshifts.

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https://api.istex.fr/ark:/67375/HCB-Z67R57T3-Z/fulltext.pdf

DOI: 10.1007/11816102_65

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<front><div type="abstract" xml:lang="en">Abstract: Ribosomal frameshifting at a particular site can yield two protein products from one coding sequence or one protein product from two overlapping open reading frames. Many organisms are known to utilize ribosomal frameshifting to express a minority of genes. However, finding ribosomal frameshift sites by a computational method is difficult because frameshift signals are diverse and dependent on the organisms and environments. There are few computer programs available for public use to identify frameshift sites from genomic sequences. We have developed a web-based application program called FSFinder2 for predicting frameshift sites of general type. We tested FSFinder2 on the Escherichia coli K12 genome to detect potential -1 frameshifting genes. From the genome sequence, we identified 18,401 frameshift sites following the X XXY YYZ motif. 11,530 frameshift sites out of the 18,401 sites include secondary structures. Comparison with the GenBank annotation produced 11 potential frameshift sites, including 3 known frameshift sites. The program is useful for analyzing frameshifts of various types and for discovering new genes expressed by frameshifts.</div>
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Prediction of Ribosomal -1 Frameshifts in the Escherichia coli K12 Genome

Prediction of Ribosomal -1 Frameshifts in the Escherichia coli K12 Genome

Source :

Abstract

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Links to Exploration step

Le document en format XML

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