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      • Record: found
      • Abstract: found
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      Is Open Access

      The iceLogo web server and SOAP service for determining protein consensus sequences

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          Abstract

          The iceLogo web server and SOAP service implement the previously published iceLogo algorithm. iceLogo builds on probability theory to visualize protein consensus sequences in a format resembling sequence logos. Peptide sequences are compared against a reference sequence set that can be tailored to the studied system and the used protocol. As such, not only over- but also underrepresented residues can be visualized in a statistically sound manner, which further allows the user to easily analyse and interpret conserved sequence patterns in proteins. The web application and SOAP service can be found free and open to all users without the need for a login on http://iomics.ugent.be/icelogoserver/main.html.

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          • Record: found
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          The Universal Protein Resource (UniProt) in 2010

          emmanuel boutet, Claire O'Donovan, Amos Bairoch (2009)
          The primary mission of UniProt is to support biological research by maintaining a stable, comprehensive, fully classified, richly and accurately annotated protein sequence knowledgebase, with extensive cross-references and querying interfaces freely accessible to the scientific community. UniProt is produced by the UniProt Consortium which consists of groups from the European Bioinformatics Institute (EBI), the Swiss Institute of Bioinformatics (SIB) and the Protein Information Resource (PIR). UniProt is comprised of four major components, each optimized for different uses: the UniProt Archive, the UniProt Knowledgebase, the UniProt Reference Clusters and the UniProt Metagenomic and Environmental Sequence Database. UniProt is updated and distributed every 3 weeks and can be accessed online for searches or download at http://www.uniprot.org.
          Article 0 comments Cited 498 times – based on 0 reviews     Review now
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            Improved visualization of protein consensus sequences by iceLogo.

            Niklaas Colaert, Kenny Helsens, Lennart Martens … (2009)
            Article 0 comments Cited 270 times – based on 0 reviews     Review now
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              Two Sample Logo: a graphical representation of the differences between two sets of sequence alignments.

              Vladimir Vacic, Lilia Iakoucheva, Predrag Radivojac (2006)
              Two Sample Logo is a web-based tool that detects and displays statistically significant differences in position-specific symbol compositions between two sets of multiple sequence alignments. In a typical scenario, two groups of aligned sequences will share a common motif but will differ in their functional annotation. The inclusion of the background alignment provides an appropriate underlying amino acid or nucleotide distribution and addresses intersite symbol correlations. In addition, the difference detection process is sensitive to the sizes of the aligned groups. Two Sample Logo extends WebLogo, a widely-used sequence logo generator. The source code is distributed under the MIT Open Source license agreement and is available for download free of charge.
              Article 0 comments Cited 222 times – based on 0 reviews     Review now
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                Author and article information

                Journal
                Journal ID (nlm-ta): Nucleic Acids Res
                Journal ID (iso-abbrev): Nucleic Acids Res
                Journal ID (hwp): nar
                Journal ID (publisher-id): nar
                Title: Nucleic Acids Research
                Publisher: Oxford University Press
                ISSN (Print): 0305-1048
                ISSN (Electronic): 1362-4962
                Publication date (Print): 01 July 2015
                Publication date (Electronic): 20 April 2015
                Publication date PMC-release: 20 April 2015
                Volume: 43
                Issue: Web Server issue
                Pages: W543-W546
                Affiliations
                [1 ]Department of Medical Protein Research, VIB, A. Baertsoenkaai 3, B-9000 Ghent, Belgium
                [2 ]Department of Biochemistry, Faculty of Medicine and Health Sciences, Ghent University, A. Baertsoenkaai 3, B-9000 Ghent, Belgium
                Author notes
                [* ]To whom correspondence should be addressed. Tel: +32 9 264 93 58; Fax: +32 9 264 94 84; Email: lennart.martens@ 123456ugent.be
                [† ]These authors contributed equally to the paper as first authors.
                Article
                DOI: 10.1093/nar/gkv385
                PMC ID: 4489316
                PubMed ID: 25897125
                SO-VID: 99ee0c20-4140-4000-80f4-c7703ac9d3f6
                Copyright © © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.
                License:

                This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.

                History
                Date accepted : 11 April 2015
                Date revision received : 28 March 2015
                Date received : 15 February 2015
                Page count
                Pages: 4
                Categories
                Subject: Web Server issue
                Custom metadata
                cover-date 1 July 2015

                ScienceOpen disciplines: Genetics
                Data availability:
                ScienceOpen disciplines: Genetics

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