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- W2485909059 abstract "Gene prediction software is often used to predict genes in genomes through automated annotation pipelines. The success of popular gene finders like Glimmer and GeneMark is reasonably good for long genes, but often fails to predict smaller genes with lengths of 150 nucleotides or less. This is due to the statistical uncertainty associated with predicting small genes. Small open reading frames (ORFs) are expected to appear by chance far more often in a complete genome compared to longer ORFs of 1kb or more. The goal of this project was to investigate if small genes in bacteria can be found by using conservation, focusing on bacteriocin-producing genes. An algorithm was developed to quantify the conservation of each position in a DNA sequence. Alignments produced by BLAST was analysed in the custom built software orfstat, which quantified the conservation of each position of all the analysed genomic sequences. 149 intergenic, i.e. unannotated, chromosomeand plasmid sequences from the Staphylococcusand the Enterococcus genera were analysed using BLAST and orfstat, and 179 ORFs were selected as bacteriocin gene candidates. Of the 179 candidates, 8 were chosen by manual selection to be tested for antibacterial activity on 53 different bacteria in the laboratory. When orfstat precision was tested on four annotated chromosomes, the RNA-coding annotated regions were given much higher average conservations than the unannotatedand the protein-coding annotated regions. The average protein-coding annotated regions were given about the same average v vi ABSTRACT conservation as the unannotated intergenic regions. The laboratory tests for the eight final bacteriocin candidates did not show any significant inhibition of growth for any of the tested bacteria." @default.
- W2485909059 created "2016-08-23" @default.
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- W2485909059 date "2014-08-04" @default.
- W2485909059 modified "2023-09-24" @default.
- W2485909059 title "Finding small genes by conservation with a focus on bacteriocins" @default.
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