Search results for "Gene prediction"
showing 9 items of 9 documents
High-Quality Genome Assembly and Annotation of the Big-Eye Mandarin Fish (Siniperca knerii)
2020
Abstract The big-eye mandarin fish (Siniperca knerii) is an endemic species of southern China. It belongs to the family Sinipercidae, which is closely related to the well-known North American sunfish family Centrarchidae. Determining the genome sequence of S. knerii would provide a foundation for better examining its genetic diversity and population history. A novel sequenced genome of the Sinipercidae also would help in comparative study of the Centrarchidae using Siniperca as a reference. Here, we determined the genome sequence of S. knerii using 10x Genomics technology and next-generation sequencing. Paired-end sequencing on a half lane of HiSeq X platform generated 56 Gbp of raw data. R…
Hybrid sequencing approach applied to human fecal metagenomic clone libraries revealed clones with potential biotechnological applications.
2012
Natural environments represent an incredible source of microbial genetic diversity. Discovery of novel biomolecules involves biotechnological methods that often require the design and implementation of biochemical assays to screen clone libraries. However, when an assay is applied to thousands of clones, one may eventually end up with very few positive clones which, in most of the cases, have to be "domesticated" for downstream characterization and application, and this makes screening both laborious and expensive. The negative clones, which are not considered by the selected assay, may also have biotechnological potential; however, unfortunately they would remain unexplored. Knowledge of t…
Chromosome-scale assembly of the yellow mealworm genome
2022
Background: The yellow mealworm beetle, Tenebrio molitor, is a promising alternative protein source for animal and human nutrition and its farming involves relatively low environmental costs. For these reasons, its industrial scale production started this century. However, to optimize and breed sustainable new T. molitor lines, the access to its genome remains essential. Methods: By combining Oxford Nanopore and Illumina Hi-C data, we constructed a high-quality chromosome-scale assembly of T. molitor. Then, we combined RNA-seq data and available coleoptera proteomes for gene prediction with GMOVE. Results: We produced a high-quality genome with a N50 = 21.9Mb with a completeness of 99.5% an…
CRISPR sequences are sometimes erroneously translated and can contaminate public databases with spurious proteins containing spaced repeats
2020
© The Author(s) 2020.
AnABlast: Re-searching for Protein-Coding Sequences in Genomic Regions
2019
AnABlast is a computational tool that highlights protein-coding regions within intergenic and intronic DNA sequences which escape detection by standard gene prediction algorithms. DNA sequences with small protein-coding genes or exons, complex intron-containing genes, or degenerated DNA fragments are efficiently targeted by AnABlast. Furthermore, this algorithm is particularly useful in detecting protein-coding sequences with nonsignificant homologs to sequences in databases. AnABlast can be executed online at http://www.bioinfocabd.upo.es/anablast/ .
Current bioinformatics tools in genomic biomedical research (Review).
2006
On the advent of a completely assembled human genome, modern biology and molecular medicine stepped into an era of increasingly rich sequence database information and high-throughput genomic analysis. However, as sequence entries in the major genomic databases currently rise exponentially, the gap between available, deposited sequence data and analysis by means of conventional molecular biology is rapidly widening, making new approaches of high-throughput genomic analysis necessary. At present, the only effective way to keep abreast of the dramatic increase in sequence and related information is to apply biocomputational approaches. Thus, over recent years, the field of bioinformatics has r…
Genome and phenotype microarray analyses of rhodococcus sp. BCP1 and rhodococcus opacus R7: Genetic determinants and metabolic abilities with environ…
2015
In this paper comparative genome and phenotype microarray analyses of Rhodococcus sp. BCP1 and Rhodococcus opacus R7 were performed. Rhodococcus sp. BCP1 was selected for its ability to grow on short-chain n-alkanes and R. opacus R7 was isolated for its ability to grow on naphthalene and on o-xylene. Results of genome comparison, includ- ing BCP1, R7, along with other Rhodococcus reference strains, showed that at least 30% of the genome of each strain presented unique sequences and only 50% of the predicted proteome was shared. To associate genomic features with metabolic capabilities of BCP1 and R7 strains, hundreds of different growth conditions were tested through Phenotype Microarray, b…
Transforming RNA-Seq Data to Improve the Performance of Prognostic Gene Signatures
2014
Gene expression measurements have successfully been used for building prognostic signatures, i.e for identifying a short list of important genes that can predict patient outcome. Mostly microarray measurements have been considered, and there is little advice available for building multivariable risk prediction models from RNA-Seq data. We specifically consider penalized regression techniques, such as the lasso and componentwise boosting, which can simultaneously consider all measurements and provide both, multivariable regression models for prediction and automated variable selection. However, they might be affected by the typical skewness, mean-variance-dependency or extreme values of RNA-…
Identification of factors involved in dimorphism and pathogenicity of Zymoseptoria tritici
2017
A forward genetics approach was applied in order to investigate the molecular basis of morphological transition in the wheat pathogenic fungus Zymoseptoria tritici. Z. tritici is a dimorphic plant pathogen displaying environmentally regulated morphogenetic transition between yeast-like and hyphal growth. Considering the infection mode of Z. tritici, the switching to hyphal growth is essential for pathogenicity allowing the fungus the host invasion through natural openings like stomata. We exploited a previously developed Agrobacterium tumefaciens-mediated transformation (ATMT) to generate a mutant library by insertional mutagenesis including more than 10,000 random mutants. To identify gene…