HIV Databases HIV Databases home HIV Databases home
HIV sequence database

Epilign Explanation


Input should consist of a single amino acid sequence. Input sequence lengths of approximately 8 to 200 amino acids work well. Sequences of slightly shorter or longer lengths may be accepted. The tool may have difficulty finding the correct alignment of sequences <8 amino acids. Long sequences will result in a wide output page.

Input 'Squeeze Gaps' Option

The 'squeeze gaps' option is useful for aligning immunologically reactive epitopes, because in such cases it is important to maintain the alignment of the C-terminal anchor residues.

If the "Squeeze Gaps" output option is selected then gaps placed to bring sequences into alignment will be squeezed out and the alignment shifted rightwards (toward the C-terminal end). For example, suppose your query has a one-amino acid insertion relative to most other sequences, then using "." as the gap character and "-" to indicate identity, the alignment

ref    ---.---

would be printed as

ref    QVAR---

The 'E' is an insertion in the query relative to other sequences. The 'Q' is the amino acid one position to the left of the V. As a result of squeezing gaps and shifting characters rightward, alignments in gappy regions will look "bad".


The output of the tool will present the following data and options:

last modified: Mon Dec 17 15:35 2007

Questions or comments? Contact us at

Operated by Los Alamos National Security, LLC, for the U.S. Department of Energy's National Nuclear Security Administration
Copyright © 2005-2017 LANS, LLC All rights reserved | Disclaimer/Privacy

Dept of Health & Human Services Los Alamos National Institutes of Health