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HFV Ebola sequence database


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 or upload your sequence(s). The options are described in the Explanation below.

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

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 acids

Note: This program is computationally intensive and may take some time to complete.
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 genes that 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 computationally intensive. An input file that is pre-aligned and smaller than 500 Kb will run immediately (no e-mail, unless you chose the option to always e-mail the result). If your input file exceeds the limit, or if your sequences required aligning, your job will be run in batch, and you will receive an e-mail with a link to your results.


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