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      HMMER web server: 2018 update

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          Abstract

          The HMMER webserver [ http://www.ebi.ac.uk/Tools/hmmer] is a free-to-use service which provides fast searches against widely used sequence databases and profile hidden Markov model (HMM) libraries using the HMMER software suite ( http://hmmer.org). The results of a sequence search may be summarized in a number of ways, allowing users to view and filter the significant hits by domain architecture or taxonomy. For large scale usage, we provide an application programmatic interface (API) which has been expanded in scope, such that all result presentations are available via both HTML and API. Furthermore, we have refactored our JavaScript visualization library to provide standalone components for different result representations. These consume the aforementioned API and can be integrated into third-party websites. The range of databases that can be searched against has been expanded, adding four sequence datasets (12 in total) and one profile HMM library (6 in total). To help users explore the biological context of their results, and to discover new data resources, search results are now supplemented with cross references to other EMBL-EBI databases.

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          Profile hidden Markov models.

          S. Eddy (1998)
          The recent literature on profile hidden Markov model (profile HMM) methods and software is reviewed. Profile HMMs turn a multiple sequence alignment into a position-specific scoring system suitable for searching databases for remotely homologous sequences. Profile HMM analyses complement standard pairwise comparison methods for large-scale sequence analysis. Several software implementations and two large libraries of profile HMMs of common protein domains are available. HMM methods performed comparably to threading methods in the CASP2 structure prediction exercise.
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            HMMER web server: 2015 update

            Robert D. Finn, Jody Clements, William Arndt … (2015)
            The HMMER website, available at http://www.ebi.ac.uk/Tools/hmmer/, provides access to the protein homology search algorithms found in the HMMER software suite. Since the first release of the website in 2011, the search repertoire has been expanded to include the iterative search algorithm, jackhmmer. The continued growth of the target sequence databases means that traditional tabular representations of significant sequence hits can be overwhelming to the user. Consequently, additional ways of presenting homology search results have been developed, allowing them to be summarised according to taxonomic distribution or domain architecture. The taxonomy and domain architecture representations can be used in combination to filter the results according to the needs of a user. Searches can also be restricted prior to submission using a new taxonomic filter, which not only ensures that the results are specific to the requested taxonomic group, but also improves search performance. The repertoire of profile hidden Markov model libraries, which are used for annotation of query sequences with protein families and domains, has been expanded to include the libraries from CATH-Gene3D, PIRSF, Superfamily and TIGRFAMs. Finally, we discuss the relocation of the HMMER webserver to the European Bioinformatics Institute and the potential impact that this will have.
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              TreeFam v9: a new website, more species and orthology-on-the-fly

              Fabian Schreiber, Mateus Patricio, Matthieu Muffato … (2013)
              TreeFam (http://www.treefam.org) is a database of phylogenetic trees inferred from animal genomes. For every TreeFam family we provide homology predictions together with the evolutionary history of the genes. Here we describe an update of the TreeFam database. The TreeFam project was resurrected in 2012 and has seen two releases since. The latest release (TreeFam 9) was made available in March 2013. It has orthology predictions and gene trees for 109 species in 15 736 families covering ∼2.2 million sequences. With release 9 we made modifications to our production pipeline and redesigned our website with improved gene tree visualizations and Wikipedia integration. Furthermore, we now provide an HMM-based sequence search that places a user-provided protein sequence into a TreeFam gene tree and provides quick orthology prediction. The tool uses Mafft and RAxML for the fast insertion into a reference alignment and tree, respectively. Besides the aforementioned technical improvements, we present a new approach to visualize gene trees and alternative displays that focuses on showing homology information from a species tree point of view. From release 9 onwards, TreeFam is now hosted at the EBI.
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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): 02 July 2018
                Publication date (Electronic): 14 June 2018
                Publication date PMC-release: 14 June 2018
                Volume: 46
                Issue: Web Server issue
                Pages: W200-W204
                Affiliations
                [1 ]EMBL-EBI European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
                [2 ]Howard Hughes Medical Institute, Harvard University, 16 Divinity Avenue, Cambridge, MA 02138, USA
                Author notes
                To whom correspondence should be addressed. Tel: +44 1223 492679; Fax: +44 1223 494468; Email: rdf@ 123456ebi.ac.uk

                The authors wish it to be known that, in their opinion, the first two authors should be regarded as Joint First Authors.

                Author information
                http://orcid.org/0000-0003-4208-4102
                http://orcid.org/0000-0001-6676-4706
                http://orcid.org/0000-0001-8626-2148
                Article
                Publisher ID: gky448
                DOI: 10.1093/nar/gky448
                PMC ID: 6030962
                PubMed ID: 29905871
                SO-VID: 1a7933bf-e2d8-4073-9f4d-a8c167837c31
                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 Non-Commercial License ( http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@ 123456oup.com

                History
                Date accepted : 12 June 2018
                Date revision received : 18 April 2018
                Date received : 13 March 2018
                Page count
                Pages: 5
                Funding
                Funded by: Howard Hughes Medical Institute 10.13039/100000011
                Award ID: R01 HG009116
                Categories
                Subject: Web Server Issue

                ScienceOpen disciplines: Genetics
                Data availability:
                ScienceOpen disciplines: Genetics

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