QuickAlign

Purpose: QuickAlign produces an alignment of a desired region from our Web alignments , with or without the incorporation of user-provided sequence(s).

Extract alignment(s) based on user-provided sequence(s): Provide one or more nucleotide or protein sequences in any standard format and the tool will align each one to the appropriate HIV alignment. This tool can be used to align epitopes, functional domains, primers, or any region of interest. If multiple input sequences are used, they do not need to be aligned or from the same region. The output will be trimmed to the region(s) of the provided sequences. If nucleotide sequences are provided, the reverse complement of the sequences will also be considered when making the best match to our alignments. If a reverse-complement sequence has a better match score than the original query sequence, then the aligned position of the reverse-complement sequence will be used to retrieve the alignment, instead of the direct sequence match.

Extract an alignment from coordinates: Enter coordinate values (either coordinates relative to the complete HIV sequence, or relative to any gene) and the tool will extract an alignment encompassing just the region of these coordinates.

Help: Explanation files are available for QuickAlign Options and for QuickAlign Results. A list of reference sequence coordinates for the genes and regions of HIV is available on the Gene Map page.