How do I find where my sequence is located in a gene or protein (for example, where are the boundaries of PCR primer or a CTL epitope)?
We recommend the use of HXB2 as a reference strain, and have developed a tool called HIV/SIV Sequence Locator, which determines the position number boundaries of a stretch of sequence, or alternatively identifies the stretch of sequence which corresponds to specified positions. You can also use this tool to identify which coordinates you need to use to find the region in the database that corresponds to your sequence; the numbering system in the search interface is based on the same method.
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