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HFV Ebola sequence database
 

Site Map & Tools

For more information, mouse over the links.

Sequence Searches

o Search Interface: Filoviruses retrieves filovirus virus sequences

o Search Interface: HFV retrieves sequences for all hemorrhagic fever viruses

o Advanced Search creates a customized search interface

Alignments

o Filovirus Premade Alignments are manually optimized alignments for viruses that belong to Ebolavirus, Marburgvirus, and Cuevavirus genera

o HFV Premade Alignments are manually optimized genus reference alignments for all hemorrhagic fever viruses

Immunology Resources

o Ebolavirus and Marburgvirus Immunology Resources provides information about filovirus T-cell epitopes and antibodies

o Epitope Maps show the location of ebolavirus and marburgvirus epitopes, relative to reference sequences

Geography Resources

o Global Outbreak Maps show global distribution of Ebola & Marburg diseases

o Geography Search: Filoviruses retrieves filovirus sequences based on geographical distribution

o Geography Search: HFV retrieves HFV sequences based on geographical distribution

Genome Coordinate Resources

o Genome Coordinate Resources provides genome coordinates and spreadsheet data for features of filovirus sequences

o Filovirus Coordinates and Naming provides information about the ebolavirus reference sequence and the sequence naming systems used for all filoviruses on this website

Sequence Manipulation Tools

o AnalyzeAlign shows weblogos, calculates frequency by position, and finds variants in an alignment

o CodonAlign takes nucleotide alignment and returns codon alignment and translates to protein sequences

o Consensus computes a customizable consensus

o Gapstreeze removes columns with more than a given % of gaps

o ElimDupes removes duplicate sequences from an alignment

o HFValign aligns your sequence(s) using either the multiple alignment program MAFFT, or using the appropriate hidden Markov model.

o PeptGen generates overlapping peptides from a protein sequence

o Pixel generates a PNG image of an alignment using 1 or more colored pixel(s) for each residue

o QuickAlign aligns short nucleotide or protein sequences (e.g., primers, epitopes) to our prebuilt genome or protein alignments, or to a user alignment

o Sequence Locator aligns your nucleotide or protein sequence to a reference genome and shows feature and coordinate information

o Translate nucleotide sequences to 1-letter amino acids

Format and Display Tools

o Ebola Genome Browser provides interactive views of the ebolavirus genome and proteome

o Genome Mapper creates a genomic feature map for any HFV organism

o Format Converter converts between 18 standard sequence formats

o SeqPublish is to make publication-ready alignments

Analysis Tools

o HFV BLAST finds sequences similar to yours in the HFV database.

o Highlighter shows matches, mismatches and mutations in an aligned set of nucleotide sequences.

o N-Glycosite find potential N-linked glycosylation sites in a protein alignment

o PCOORD multidimensional analysis of sequence variation

o SNAP calculates synonymous/non-synonymous substitution rates

o VESPA detects signatures: residues with different frequencies in two sequence sets

Phylogenetics Tools

o FindModel finds which evolutionary model best fits your sequences

o PhyloPlace reports phylogenetic relatedness of query sequence with reference sequences in known clades.

o PhyML interface creates and displays a Maximum-Likelihood tree using the PhyML code; many evolutionary models can be specified

o Rainbow Tree color codes phylogenetic tree branches according to labels in the sequence names

o TreeMaker generates a quick-and-dirty phylogenetic tree

o TreeRate calculates branch lengths between internal and end nodes based on a Newick treefile

External Tools and Resources

o External Resources links to additional resources on other websites




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