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HFV Ebola sequence database
 

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HFVAlign

VirAlign for HFV sequences

Purpose: HFValign takes aligned or unaligned nucleotide sequences and gives the alignment of pre-defined regions of an appropriate reference sequence. If your sequences aren't pre-aligned, this tool can align them via a Hidden Markov Model or MAFFT.

Usage: Paste your sequence(s) into the space provided, or browse for your file. Then you may choose options.

Explanation: Please read the Explanation below before using.

Input
Paste your sequence(s)
Or upload your sequence file
Select feature
Select virus
Let program pick
Use     Family/genus
Species

Options
Always e-mail result
Align the sequences       By HMM-align     By MAFFT
Check reverse complement
Codon-Align the sequences        Allow codons to compensate frameshift
Insert a reference sequence       
Translate to amino acid

Note: This program is computationally intensive and may take a while to run. Please don't resubmit your request!

Explanation: HFValign aligns input sequences to a reference sequences and clips the regions the input touched. There are five options:

HFValign attempts to automatically recognize the format of your input file by using Format Converter. The results page summarizes the running parameters and information about the input, and gives you the alignment of the region which the input touched . From this page you can download the alignment in different formats, or send the resulting alignment to TreeMaker or FindModel.

Aligning large sequences is a computationally intensive procedure. An input file that is pre-aligned and smaller than 500 Kb is run immediately. If your input file exceeds the limit, or if you checked the 'Align' option , your job will be run in batch, and you will receive an email when it has finished. The email contains link to your results.

References:




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