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

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About: Prediction of Ribosomal -1 Frameshifts in the Escherichia coli K12 Genome Goto Sponge NotDistinct Permalink

An Entity of Type : schema:ScholarlyArticle, within Data Space : wasabi.inria.fr associated with source document(s)

Attributes	Values
type	Academic Article research paper schema:ScholarlyArticle
isDefinedBy	Covid-on-the-Web dataset
title	Prediction of Ribosomal -1 Frameshifts in the Escherichia coli K12 Genome
Creator	Han, Kyungsook Byun, Yanga Moon, Sanghoon
topic	covid:937b665c34abde05316890a5a9029c4052c9479e#this
source	PMC
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.
has issue date	2006-01-01(xsd:dateTime)
bibo:doi	10.1007/11816102_65
has license	no-cc
sha1sum (hex)	937b665c34abde05316890a5a9029c4052c9479e
schema:url	https://doi.org/10.1007/11816102_65
resource representing a document's title	Prediction of Ribosomal -1 Frameshifts in the Escherichia coli K12 Genome
has PubMed Central identifier	PMC7122894
schema:publication	Computational Intelligence and Bioinformatics
resource representing a document's body	covid:937b665c34abde05316890a5a9029c4052c9479e#body_text
is http://vocab.deri.ie/void#inDataset of	https://covidontheweb.inria.fr:4443/about/id/http/ns.inria.fr/covid19/937b665c34abde05316890a5a9029c4052c9479e
is schema:about of	named entity 'ESCHERICHIA COLI K12' named entity 'ribosomal frameshift' named entity 'frameshifts' named entity 'motif' named entity 'web-based application' named entity 'yield' named entity 'Comparison' named entity 'RIBOSOMAL' named entity 'GENOME' named entity 'AVAILABLE' named entity 'TO EXPRESS' named entity 'POTENTIAL' named entity 'FINDING' named entity 'DEPENDENT' named entity 'YIELD' named entity 'HAVE' named entity 'COMPUTER PROGRAMS' named entity 'GENOMIC' named entity 'TESTED' named entity 'IDENTIFIED' named entity 'PRODUCT' named entity 'CODING SEQUENCE' named entity 'KNOWN' named entity 'TYPES' named entity 'SITE' named entity 'RIBOSOMAL FRAMESHIFT' named entity 'PREDICTION' named entity 'STRUCTURES' named entity 'PROGRAM' named entity 'OVERLAPPING' named entity 'NEW' named entity 'TO IDENTIFY' named entity 'ESCHERICHIA COLI K12' named entity 'PREDICTING' named entity 'COMPUTATIONAL METHOD' named entity 'GENOME' named entity 'OPEN READING FRAMES' named entity 'PARTICULAR' named entity 'VARIOUS' named entity 'DIFFICULT' named entity 'ENVIRONMENTS' named entity 'USE' named entity 'EXPRESSED' named entity 'PUBLIC' named entity 'GENOME SEQUENCE' named entity 'APPLICATION PROGRAM' named entity 'PROTEIN ' named entity 'MOTIF' named entity 'ANALYZING' named entity 'GENERAL' named entity 'MINORITY' named entity 'SEQUENCES' named entity 'ORGANISMS' named entity 'COMPARISON' named entity 'PRODUCTS' named entity 'TO DETECT' named entity 'INCLUDING' named entity 'RIBOSOMAL' named entity 'USEFUL' named entity 'FOLLOWING' named entity 'SIGNALS' named entity 'GENES' named entity 'DIVERSE' named entity 'SECONDARY' named entity 'GENBANK' named entity 'TYPE' named entity 'INCLUDE' named entity 'FRAMESHIFT' named entity 'ANNOTATION' covid:arg/937b665c34abde05316890a5a9029c4052c9479e named entity 'XXY' named entity 'frameshifting' named entity 'protein' named entity 'frameshift' named entity 'Escherichia coli' named entity 'frameshift' named entity 'detect' named entity 'protein' named entity 'secondary structures'

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