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. 2018 Jul 2;46(W1):W200-W204.
doi: 10.1093/nar/gky448.

HMMER web server: 2018 update

Simon C Potter  1 , Aurélien Luciani  1 , Sean R Eddy  2 , Youngmi Park  1 , Rodrigo Lopez  1 , Robert D Finn  1
Affiliations

HMMER web server: 2018 update

Simon C Potter et al. Nucleic Acids Res. .

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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Figures

Figure 1.
Figure 1.
Results of a search in the ‘score’ view with the new ‘Cross references’ column, populated with links to the hit sequence in other EMBL-EBI databases. As the page is loaded, these symbols may disappear if no cross-references are found in this category.
Figure 2.
Figure 2.
New taxonomy view. The tree is navigable via keyboard or mouse, with the red circle showing the currently selected node, and the size of the blue circles being proportional to the number of hits. Figure 3. As the user changes the selected node, the red line highlights the selected route to the node. The lineage is shown below the figure and the small barchart shows the distribution of E-values at the selected node.
Figure 3.
Figure 3.
Annotation of the domain graphic with the catalytic active sites predicted by Pfam, with extra information about the middle site displayed in a mouse-activated pop-up.
See this image and copyright information in PMC

References

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    1. Finn R.D., Coggill P., Eberhardt R.Y., Eddy S.R., Mistry J., Mitchell A.L., Potter S.C., Punta M., Qureshi M., Sangrador-Vegas A. et al. . The Pfam protein families database: towards a more sustainable future. Nucleic Acids Res. 2016; 44:D279–D285. - PMC - PubMed
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    1. Finn R.D., Clements J., Eddy S.R.. HMMER web server: interactive sequence similarity searching. Nucleic Acids Res. 2011; 39:W29–W37. - PMC - PubMed
    1. Finn R.D., Clements J., Arndt W., Miller B.L., Wheeler T.J., Schreiber F., Bateman A., Eddy S.R.. HMMER web server: 2015 update. Nucleic Acids Res. 2015; 43:W30–W38. - PMC - PubMed

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