Articles producció científica> Bioquímica i Biotecnologia

PairWise Neighbours database: overlaps and spacers among prokaryote genomes

  • Identification data

    Identifier: imarina:5122196
    Authors:
    Pallejà A, Reverter T, Garcia-Vallvé S, Romeu A.
    Abstract:
    Background: Although prokaryotes live in a variety of habitats and possess different metabolic and genomic complexity, they have several genomic architectural features in common. The overlapping genes are a common feature of the prokaryote genomes. The overlapping lengths tend to be short because as the overlaps become longer they have more risk of deleterious mutations. The spacers between genes tend to be short too because of the tendency to reduce the non coding DNA among prokaryotes. However they must be long enough to maintain essential regulatory signals such as the Shine-Dalgarno (SD) sequence, which is responsible of an efficient translation. Description: PairWise Neighbours is an interactive and intuitive database used for retrieving information about the spacers and overlapping genes among bacterial and archaeal genomes. It contains 1,956,294 gene pairs from 678 fully sequenced prokaryote genomes and is freely available at the URL http://genomes.urv.cat/pwneigh. This database provides information about the overlaps and their conservation across species. Furthermore, it allows the wide analysis of the intergenic regions providing useful information such as the location and strength of the SD sequence. Conclusion: There are experiments and bioinformatic analysis that rely on correct annotations of the initiation site. Therefore, a database that studies the overlaps and spacers among prokaryotes appears to be desirable. PairWise Neighbours database permits the reliability analysis of the overlapping structures and the study of the SD presence and location among the adjacent genes, which may help to check the annotation of the initiation sites.
  • Others:

    Author, as appears in the article.: Pallejà A, Reverter T, Garcia-Vallvé S, Romeu A.
    Department: Bioquímica i Biotecnologia
    e-ISSN: 1471-2164
    URV's Author/s: Garcia Vallve, Santiago / ROMEU FIGUEROLA, ANTONIO RAMÓN
    Keywords: Translation initiation Shine-dalgarno sequence Prediction Operon Gene overlaps Expression Evolution Escherichia-coli Codon Bacteria
    Abstract: Background: Although prokaryotes live in a variety of habitats and possess different metabolic and genomic complexity, they have several genomic architectural features in common. The overlapping genes are a common feature of the prokaryote genomes. The overlapping lengths tend to be short because as the overlaps become longer they have more risk of deleterious mutations. The spacers between genes tend to be short too because of the tendency to reduce the non coding DNA among prokaryotes. However they must be long enough to maintain essential regulatory signals such as the Shine-Dalgarno (SD) sequence, which is responsible of an efficient translation. Description: PairWise Neighbours is an interactive and intuitive database used for retrieving information about the spacers and overlapping genes among bacterial and archaeal genomes. It contains 1,956,294 gene pairs from 678 fully sequenced prokaryote genomes and is freely available at the URL http://genomes.urv.cat/pwneigh. This database provides information about the overlaps and their conservation across species. Furthermore, it allows the wide analysis of the intergenic regions providing useful information such as the location and strength of the SD sequence. Conclusion: There are experiments and bioinformatic analysis that rely on correct annotations of the initiation site. Therefore, a database that studies the overlaps and spacers among prokaryotes appears to be desirable. PairWise Neighbours database permits the reliability analysis of the overlapping structures and the study of the SD presence and location among the adjacent genes, which may help to check the annotation of the initiation sites.
    Thematic Areas: Zootecnia / recursos pesqueiros Saúde coletiva Química Odontología Medicina veterinaria Medicina iii Medicina ii Medicina i Matemática / probabilidade e estatística Interdisciplinar Genetics & heredity Genetics Farmacia Engenharias iv Engenharias iii Engenharias ii Educação física Ciências biológicas iii Ciências biológicas ii Ciências biológicas i Ciências ambientais Ciências agrárias i Ciência de alimentos Ciência da computação Biotecnología Biotechnology & applied microbiology Biotechnology Biodiversidade Astronomia / física
    licence for use: https://creativecommons.org/licenses/by/3.0/es/
    Author's mail: santi.garcia-vallve@urv.cat
    Author identifier: 0000-0002-0348-7497
    Record's date: 2023-02-18
    Journal volume: 10
    Papper version: info:eu-repo/semantics/publishedVersion
    Papper original source: Bmc Genomics. 10
    APA: Pallejà A, Reverter T, Garcia-Vallvé S, Romeu A. (2009). PairWise Neighbours database: overlaps and spacers among prokaryote genomes. Bmc Genomics, 10(), -. DOI: 10.1186/1471-2164-10-281
    Licence document URL: https://repositori.urv.cat/ca/proteccio-de-dades/
    Entity: Universitat Rovira i Virgili
    Journal publication year: 2009
    Publication Type: Journal Publications
  • Keywords:

    Biotechnology,Biotechnology & Applied Microbiology,Genetics,Genetics & Heredity
    Translation initiation
    Shine-dalgarno sequence
    Prediction
    Operon
    Gene overlaps
    Expression
    Evolution
    Escherichia-coli
    Codon
    Bacteria
    Zootecnia / recursos pesqueiros
    Saúde coletiva
    Química
    Odontología
    Medicina veterinaria
    Medicina iii
    Medicina ii
    Medicina i
    Matemática / probabilidade e estatística
    Interdisciplinar
    Genetics & heredity
    Genetics
    Farmacia
    Engenharias iv
    Engenharias iii
    Engenharias ii
    Educação física
    Ciências biológicas iii
    Ciências biológicas ii
    Ciências biológicas i
    Ciências ambientais
    Ciências agrárias i
    Ciência de alimentos
    Ciência da computação
    Biotecnología
    Biotechnology & applied microbiology
    Biotechnology
    Biodiversidade
    Astronomia / física
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