Alignment Slicer Help
The Alignment Slicer cuts slices from multiple sequence alignments.
The inputs and options are described below.
- One DNA or amino acid alignment.
- Any organism.
Breakpoints define the points where you want the alignment
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
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.
last modified: Thu Nov 21 10:00 2013