Explanation of QuickAlign Options

Delete Gaps Option

If the "Delete 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 HIVs, then using "-" as the gap character, the following alignment

QUERY  VARELHP
HXB2   VAR-LHP
seq2   VAR-LHP
seq3   VAR-LFP
etc...

would be like this with gaps deleted

seqx  VARELHP
HXB2  QVARLHP
seq2  QVARLHP
seq3  QVARLFP
etc...

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, such as the V3 loop of gp160 will look "bad."

The delete 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. Epitopes don't contain gaps.

Reverse Complement Option

If you select this option, QuickAlign will locate the best match position of your query in the HXB2 genome. It will then reverse complement the query and locate its position. If the match score for the reverse complement is higher than the query itself, then the reverse complement position will be used to extract the alignment. The reverse complement option is ignored when the query is a protein.

Do Wide Output Option

QuickAlign presents its alignment result in "output-aligned" format which normally looks like this:

For ease of reading, the alignment is presented in groups of 10 characters, a space, then 10 more characters, etc. up to a maximum line width of 50 characters. If the query is longer than 50 characters, it will be continued below. However, you can force lines to be longer than 50 characters, by checking "Yes" in the Do Wide Output Option.