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PlaToLoCo: the first web meta-server for visualization and annotation of low complexity regions in proteins.
Jarnot, Patryk; Ziemska-Legiecka, Joanna; Dobson, Laszlo; Merski, Matthew; Mier, Pablo; Andrade-Navarro, Miguel A; Hancock, John M; Dosztányi, Zsuzsanna; Paladin, Lisanna; Necci, Marco; Piovesan, Damiano; Tosatto, Silvio C E; Promponas, Vasilis J; Grynberg, Marcin; Gruca, Aleksandra.
Afiliação
  • Jarnot P; Department of Computer Networks and Systems, Silesian University of Technology, Akademicka 16, 44-100 Gliwice, Poland.
  • Ziemska-Legiecka J; Institute of Biochemistry and Biophysics PAS, Pawinskiego 5A, 02-106 Warsaw, Poland.
  • Dobson L; Faculty of Information Technology and Bionics, Pázmány Péter Catholic University, Práter u. 50/A, 1083 Budapest, Hungary.
  • Merski M; Research Centre for Natural Sciences, Magyar Tudósok Körútja 2, 1117 Budapest, Hungary.
  • Mier P; Structural Biology Group, Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, Zwirki i Wigury 101, 02-089 Warsaw, Poland.
  • Andrade-Navarro MA; Faculty of Biology, Johannes Gutenberg University Mainz, Hans-Dieter-Hüsch-Weg 15, 55128 Mainz, Germany.
  • Hancock JM; Faculty of Biology, Johannes Gutenberg University Mainz, Hans-Dieter-Hüsch-Weg 15, 55128 Mainz, Germany.
  • Dosztányi Z; ELIXIR, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK.
  • Paladin L; Department of Biochemistry, ELTE Eötvös LorándUniversity, Budapest, Pázmány Péter stny 1/c 1117, Budapest, Hungary.
  • Necci M; Department of Biomedical Sciences, University of Padova, Via Ugo Bassi 58/B, 35131 Padova, Italy.
  • Piovesan D; Department of Biomedical Sciences, University of Padova, Via Ugo Bassi 58/B, 35131 Padova, Italy.
  • Tosatto SCE; Department of Biomedical Sciences, University of Padova, Via Ugo Bassi 58/B, 35131 Padova, Italy.
  • Promponas VJ; Department of Biomedical Sciences, University of Padova, Via Ugo Bassi 58/B, 35131 Padova, Italy.
  • Grynberg M; Bioinformatics Research Laboratory, Department of Biological Sciences, University of Cyprus, P.O. Box 20537, Nicosia, CY 1678, Cyprus.
  • Gruca A; Institute of Biochemistry and Biophysics PAS, Pawinskiego 5A, 02-106 Warsaw, Poland.
Nucleic Acids Res ; 48(W1): W77-W84, 2020 07 02.
Article em En | MEDLINE | ID: mdl-32421769
Low complexity regions (LCRs) in protein sequences are characterized by a less diverse amino acid composition compared to typically observed sequence diversity. Recent studies have shown that LCRs may co-occur with intrinsically disordered regions, are highly conserved in many organisms, and often play important roles in protein functions and in diseases. In previous decades, several methods have been developed to identify regions with LCRs or amino acid bias, but most of them as stand-alone applications and currently there is no web-based tool which allows users to explore LCRs in protein sequences with additional functional annotations. We aim to fill this gap by providing PlaToLoCo - PLAtform of TOols for LOw COmplexity-a meta-server that integrates and collects the output of five different state-of-the-art tools for discovering LCRs and provides functional annotations such as domain detection, transmembrane segment prediction, and calculation of amino acid frequencies. In addition, the union or intersection of the results of the search on a query sequence can be obtained. By developing the PlaToLoCo meta-server, we provide the community with a fast and easily accessible tool for the analysis of LCRs with additional information included to aid the interpretation of the results. The PlaToLoCo platform is available at: http://platoloco.aei.polsl.pl/.
Assuntos

Texto completo: 1 Coleções: 01-internacional Base de dados: MEDLINE Assunto principal: Software / Proteínas Limite: Humans Idioma: En Revista: Nucleic Acids Res Ano de publicação: 2020 Tipo de documento: Article País de afiliação: Polônia

Texto completo: 1 Coleções: 01-internacional Base de dados: MEDLINE Assunto principal: Software / Proteínas Limite: Humans Idioma: En Revista: Nucleic Acids Res Ano de publicação: 2020 Tipo de documento: Article País de afiliação: Polônia