What it does

Convert BlastXML results into GFF3 format.

Options

The trimming option captures an important feature provided in this tool that isn't provided in most other BlastXML visualization tools: the fact that blast captures complete alignment location information.

This means that when most blast visualization tools produce output which looks like this:

This tool produces output which shows where the real subject sequence starts and ends relative to your sequence:

This can be a useful feature for examining alternate start locations that are used by sequences found from your blast query.

The green bars on the very top row of the picture indicate start sites, as you can see the blast hits and the genome in the visualization share an upstream start site. You don't lose the information present in your blastxml data.

So, to the end of useful functionality, this options is controllable:

• you can trim neither end, see where the real protein alignments are.
• you can trim both ends, like blasts HTML reports
• you can trim just the end of the sequence, as upstream is generally more interesting, and having long tails can result in poor visualizations.