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HFV Ebola sequence database

HFV database: Archived news

A new tool, AnalyzeAlign, is available. Input any alignment and the tool will show weblogos, calculate frequency by position, and find variants. The user may analyze the alignment as a whole, or specify subgroupings for analysis. Many options are provided to customize the weblogo image. 23 March 2015

The Ebolavirus Genome Browser is now available. It provides interactive views of the viral genome, proteome, epitope data, and more. 05 February 2015

New Global Outbreak Maps give a different perspective on the global distributions of Ebolavirus and Marburgvirus diseases. 03 February 2015

Several new resources and updates are available. Curated alignments for Ebola and Marburg sequences now include more sequences and a new alignment type with one sequence per outbreak. Ebola Immunology resources include epitope spreadsheets and maps. Ebola Annotation provides spreadsheets of feature data. 02 February 2015

Several updates are now available for Ebola. Curated alignments are available for Ebola and Marburg viruses. A new QuickAlign tool will align any Ebola sequence(s) with all sequences from our database and show frequency distributions. A Geography Search is now available specifically for Filoviridae. 24 November 2014

We are in the process of updating the Ebola sections of this website, including new sequence alignments and improved sequence search and annotation features. Please check back for updates. 05 November 2014

We have added a new tool, GenBank Entry Generation, that generates Sequin files for HFV sequences. This tool automatically generates protein annotations and includes them in the Sequin file, together with related data, for submission to GenBank. 05 October 2011

Highlighter is a tool to visualize mutations: matches, mismatches, transition and transversion mutations, and silent and non-silent mutations in a set of nucleotide sequences that are aligned and in frame. It is particularly useful for allowing visualization of potential recombination and SNPs in closely related sequences, such as those isolated from a single patient. Highlighter now also work with amino acid sequences. 24 May 2011

The icon color coding to indicate sequence orientation has changed - the icon now reflects both the orientation of reference sequence relative to the majority of the genus (genomic structure line) and the orientation of each sequence relative to the reference sequence (bar indicating sequence location). For more information and examples, go here. 20 May 2011

Annotation data in this database was augmented with manually annotated information obtained from the Flavitrack database. This database is described in Danecek, P. and Schein, C. H. (2008) BIOT and Misra, M. and Schein, C. H. (2007) Bioinformatics, 23 (19), 2645-7. 19 May 2011

We have added a large number of viral species to the database that are unclassified at the genus and/or species level. We are working on a solution for the lack of reference sequences and gene/region coordinates for these viruses, and hope to have this implemented in the next month. 18 May 2011

Manually curated alignments of the HFV reference sequences are now available at HFV Sequence Alignments. The alignments are organized by genus and by segment. They can be used as "background set" for trees and other classification tools. These alignments also form the basis for the HMM models to create the on-the-fly alignments in the search interface. 13 July 2010

A beta version of a new tool, Protein Feature Accent, is now available. This user-friendly tool allows a user to highlight regions and features of interest (e.g. resistance mutations or immune epitopes) on protein structures, to calculate and plot entropy, and to display the protein in many different ways. The tool uses Jmol, and automatically checks for and lists all 3D protein structures available in PDB. 26 February 2010

A beta version of a new tool, Protein Feature Accent, is now available. This user-friendly tool displays PDB protein structures in the browser. A list of available structures is provided, and will be automatically updated. The tool allows users to change the display modes, highlight regions of interest on protein structures, display N-linked glycosylation sites, and much more. Users can also upload their own PDB-formatted structures. 30 November 2009

Geographic distribution of search results. With this new feature of our main search interface, you can display the results of your sequence search as a map, with pies to display the geographical origins of the sequences. Use the 'Geography' button on the search results page. 21 October 2009

Site launch 06 October 2009

Questions or comments? Contact us at hfv-info@lanl.gov