HMMER web server: 2015 update

By Robert D. Finn, Jody Clements, W. Arndt, B. L. Miller, Travis J. Wheeler, Fabian Schreiber, Alex Bateman, Sean R. Eddy. 2015

1,607 citations recorded by the source corpus.

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.

Subfields: Molecular Biology, Spectroscopy

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Citations in the corpus

Evolutionary-scale prediction of atomic level protein structure with a language model (2022, background): “[47] Simon C Potter, AurÂ elien Luciani, Sean R Eddy, Youngmi Park, Rodrigo Lopez, and Robert D Finn.”
CATH: an expanded resource to predict protein function through structure and sequence (2016, methodology): “Hidden Markov model (HMM) technology (6) is then employed to create profiles, or evolutionary fingerprints, seeded from these CATH structural domains.”
The Pfam protein families database: towards a more sustainable future (2015, methodology): “Based upon our own experiences, we believe that the functionality previously provided by Pfam-B is actually far better served by taking regions that are not covered by Pfam-A entries and performing a jackhmmer search using the HMMER website (13).”
HMMER web server: 2018 update (2018, methodology): “The interface has been described in detail (5,6).”
IMG/M: integrated genome and metagenome comparative data analysis system (2016, methodology): “0, respectively (15), comparing to InterPro models using a customized version of InterproScan5 (16) and associating proteins with KEGG Ortholog (KO) terms (17) using LAST (18).”
The MEROPS database of proteolytic enzymes, their substrates and inhibitors in 2017 and a comparison with peptidases in the PANTHER database (2017, methodology): “Once the peptidase/inhibitor unit has been defined, it becomes the new family type example and it is used to search either the UniProtKB (8) or NCBI Protein sequence databases (9) with BLASTP (10) or via the HMMER 3 webserver (11).”
Using EMBL‐EBI Services via Web Interface and Programmatically via Web Services (2014, methodology): “If the job status is FINISHED, you can view the possible result types with the command: docker run --rm ebiwp/webservice-clients hmmer3_phmmer.pl --resultTypes --jobid <JobId> The HMMER3 phmmer web service provides a plain text output (out) and a plain input (sequence).”
Deep convolutional networks for quality assessment of protein folds (2018, methodology): “The families were found using HMMER [29] with an E-value cutoff of 1.0 [28].”
MitoCarta2.0: an updated inventory of mammalian mitochondrial proteins (2015, methodology): “Homology was determined by BlastP (22) top hit (Expect < 1e-3) or jackHMMER (23) reciprocal hit (see Supplementary Data).”
ICEberg 2.0: an updated database of bacterial integrative and conjugative elements (2018, methodology): “ICEfinder employs a method we called ‘Pattern-based hit co-localization’ (see the Supplementary Methods) that detects the signature sequences of the recombination modules and conjugation modules based on their profile HMMs (19) (Supplementary Table S2, S3 and Figure S4).”