Alignment Slicer Help

The Alignment Slicer cuts slices from multiple sequence alignments. The inputs and options are described below.

Alignment

• One DNA or amino acid alignment.
• Any organism.
• Any standard sequence format.

Breakpoints

• Breakpoints define the points where you want the alignment sliced.
• Each line defines 3 items: start residue, stop residue, and name of the slice.
• The 3 items in each line can be space-delimited or tab-delimited.
• To slice out a single residue, the start and stop numbers should be the same.
• All slices with the same name are merged together in the order they appear in the input.
• You can manipulate the output by changing the names. In the sample input, you could name each A segment differently (A1, A2, A3) in order to obtain each segment as a single slice, instead of getting them merged together.
• Any region not included in the breakpoints will be omitted from the output.

Residue or Alignment

Does the numbering of the breakpoints refer to the numbering of the residues in the first sequence of the alignment (ignoring gaps), or to the columns of the alignment?

Alignment start

If you want to slice a partial alignment from a larger alignment, enter the position of the start of the alignment. This position will be relative to the first sequence, or relative to the columns of the alignment, based on the choice of the option above.

Gap characters

Specify what character(s) represent gaps in your alignment. The default characters are dash (-) and tilde (~).

• The output is a set of alignments, one for each name.
• Format is Fasta.
• To download, click on the name of the alignment.

Return to Alignment Slicer input page.