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      The UNITE database for molecular identification of fungi: handling dark taxa and parallel taxonomic classifications

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          Abstract

          UNITE ( https://unite.ut.ee/) is a web-based database and sequence management environment for the molecular identification of fungi. It targets the formal fungal barcode—the nuclear ribosomal internal transcribed spacer (ITS) region—and offers all ∼1 000 000 public fungal ITS sequences for reference. These are clustered into ∼459 000 species hypotheses and assigned digital object identifiers (DOIs) to promote unambiguous reference across studies. In-house and web-based third-party sequence curation and annotation have resulted in more than 275 000 improvements to the data over the past 15 years. UNITE serves as a data provider for a range of metabarcoding software pipelines and regularly exchanges data with all major fungal sequence databases and other community resources. Recent improvements include redesigned handling of unclassifiable species hypotheses, integration with the taxonomic backbone of the Global Biodiversity Information Facility, and support for an unlimited number of parallel taxonomic classification systems.

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          Improved tools for biological sequence comparison.

          W R Pearson, D J Lipman (1988)
          We have developed three computer programs for comparisons of protein and DNA sequences. They can be used to search sequence data bases, evaluate similarity scores, and identify periodic structures based on local sequence similarity. The FASTA program is a more sensitive derivative of the FASTP program, which can be used to search protein or DNA sequence data bases and can compare a protein sequence to a DNA sequence data base by translating the DNA data base as it is searched. FASTA includes an additional step in the calculation of the initial pairwise similarity score that allows multiple regions of similarity to be joined to increase the score of related sequences. The RDF2 program can be used to evaluate the significance of similarity scores using a shuffling method that preserves local sequence composition. The LFASTA program can display all the regions of local similarity between two sequences with scores greater than a threshold, using the same scoring parameters and a similar alignment algorithm; these local similarities can be displayed as a "graphic matrix" plot or as individual alignments. In addition, these programs have been generalized to allow comparison of DNA or protein sequences based on a variety of alternative scoring matrices.
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            NCBI Reference Sequences (RefSeq): current status, new features and genome annotation policy

            Kim D. Pruitt, Tatiana Tatusova, Garth R. Brown … (2011)
            The National Center for Biotechnology Information (NCBI) Reference Sequence (RefSeq) database is a collection of genomic, transcript and protein sequence records. These records are selected and curated from public sequence archives and represent a significant reduction in redundancy compared to the volume of data archived by the International Nucleotide Sequence Database Collaboration. The database includes over 16 000 organisms, 2.4 × 106 genomic records, 13 × 106 proteins and 2 × 106 RNA records spanning prokaryotes, eukaryotes and viruses (RefSeq release 49, September 2011). The RefSeq database is maintained by a combined approach of automated analyses, collaboration and manual curation to generate an up-to-date representation of the sequence, its features, names and cross-links to related sources of information. We report here on recent growth, the status of curating the human RefSeq data set, more extensive feature annotation and current policy for eukaryotic genome annotation via the NCBI annotation pipeline. More information about the resource is available online (see http://www.ncbi.nlm.nih.gov/RefSeq/).
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              Improved software detection and extraction of ITS1 and ITS2 from ribosomal ITS sequences of fungi and other eukaryotes for analysis of environmental sequencing data

              Johan Bengtsson-Palme, Martin Ryberg, Martin Hartmann … (2013)
              Article 0 comments Cited 434 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 (publisher-id): nar
                Title: Nucleic Acids Research
                Publisher: Oxford University Press
                ISSN (Print): 0305-1048
                ISSN (Electronic): 1362-4962
                Publication date (Print): 08 January 2019
                Publication date (Electronic): 29 October 2018
                Publication date PMC-release: 29 October 2018
                Volume: 47
                Issue: Database issue , Database issue
                Pages: D259-D264
                Affiliations
                [1 ]University of Gothenburg, Department of Biological and Environmental Sciences, Gothenburg Global Biodiversity Centre, Box 461, 405 30 Gothenburg, Sweden
                [2 ]Natural History Museum, University of Oslo, P.O. Box 1172, Blindern, 0318 Oslo, Norway
                [3 ]The James Hutton Institute and University of Aberdeen, Aberdeen, UK
                [4 ]Wisconsin Institute for Discovery, University of Wisconsin-Madison, 330 North Orchard Street, Madison, WI 53715, USA
                [5 ]Centre for Antibiotic Resistance research (CARe) at University of Gothenburg, Gothenburg, Sweden
                [6 ]Department of Infectious Diseases, Sahlgrenska Academy, University of Gothenburg, Guldhedsgatan 10, SE-413 46 Gothenburg, Sweden
                [7 ]Global Biodiversity Information Facility, Universitetsparken 15, DK-2100 Copenhagen Ø, Denmark
                [8 ]Department of Plant and Microbial Biology, University of Minnesota, 1479 Gortner Avenue, St. Paul, MN 55108, USA
                [9 ]Department of Botany, National Museum of Natural History, Smithsonian Institution, Washington, DC 20013, USA
                [10 ]Jacobs University Bremen and MPI for Marine Microbiology, Celsiusstr. 1, D-28359 Bremen, Germany
                [11 ]University of Tartu, Institute of Ecology and Earth Sciences, 40 Lai Street, 51005 Tartu, Estonia
                [12 ]Natural History Museum and Botanical Garden, University of Tartu, 46 Vanemuise Street, 51003 Tartu, Estonia
                Author notes
                To whom correspondence should be addressed. Tel: +46 31 7862623; Fax: +46 31 7862560; Email: henrik.nilsson@ 123456bioenv.gu.se
                Author information
                http://orcid.org/0000-0002-6528-3158
                Article
                Publisher ID: gky1022
                DOI: 10.1093/nar/gky1022
                PMC ID: 6324048
                PubMed ID: 30371820
                SO-VID: e233bdeb-96cf-4491-85d0-7e562665e03e
                Copyright © © The Author(s) 2018. 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 : 12 October 2018
                Date revision received : 11 October 2018
                Date received : 14 September 2018
                Page count
                Pages: 6
                Funding
                Funded by: Alfred P. Sloan Foundation 10.13039/100000879
                Award ID: G-2015-14062
                Funded by: Swedish Research Council of Environment, Agricultural Sciences, and Spatial Planning 10.13039/501100004359
                Award ID: 215-2011-498
                Categories
                Subject: Database Issue

                ScienceOpen disciplines: Genetics
                Data availability:
                ScienceOpen disciplines: Genetics

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