2015 | Robert D. Finn, Jody Clements, William Arndt, Benjamin L. Miller, Travis J. Wheeler, Fabian Schreiber, Alex Bateman, Sean R. Eddy
The HMMER web server, available at http://www.ebi.ac.uk/Tools/hmmmer/, provides access to protein homology search algorithms. Since its initial release in 2011, the server has expanded its capabilities to include iterative search algorithms like jackhmmer and additional profile hidden Markov model (HMM) libraries from CATH-Gene3D, PIRSF, Superfamily, and TIGRFAMs. The server has also introduced new ways to present homology search results, such as taxonomic distribution and domain architecture representations, which can be used to filter results according to user needs. The server now primarily focuses on UniProtKB, the world's premier protein database, and includes subsets for high-quality annotations, representative sets, and curated sequences. The article discusses the improvements in search performance, the expanded repertoire of HMM libraries, and the development of alternative result visualizations, including the 'Sequence Matches and Features' section, which provides detailed annotations and summaries of search results. The server also supports filtering results using taxonomy and domain architecture views, and allows for taxonomically restricted searches to reduce the initial search space. The article concludes by discussing the relocation of the HMMER web server to the European Bioinformatics Institute (EMBL-EBI) and the benefits of this move, including improved scalability and synchronization with target database updates.The HMMER web server, available at http://www.ebi.ac.uk/Tools/hmmmer/, provides access to protein homology search algorithms. Since its initial release in 2011, the server has expanded its capabilities to include iterative search algorithms like jackhmmer and additional profile hidden Markov model (HMM) libraries from CATH-Gene3D, PIRSF, Superfamily, and TIGRFAMs. The server has also introduced new ways to present homology search results, such as taxonomic distribution and domain architecture representations, which can be used to filter results according to user needs. The server now primarily focuses on UniProtKB, the world's premier protein database, and includes subsets for high-quality annotations, representative sets, and curated sequences. The article discusses the improvements in search performance, the expanded repertoire of HMM libraries, and the development of alternative result visualizations, including the 'Sequence Matches and Features' section, which provides detailed annotations and summaries of search results. The server also supports filtering results using taxonomy and domain architecture views, and allows for taxonomically restricted searches to reduce the initial search space. The article concludes by discussing the relocation of the HMMER web server to the European Bioinformatics Institute (EMBL-EBI) and the benefits of this move, including improved scalability and synchronization with target database updates.