Output Formats
Twine was written to allow easy visualization of enhancer
information. Manual annotation is a pain, and you can easily miss
stuff.
Some programs have graphical outputs, but they're generally static
images. Fortunately, some people wrote a very nice library
for Java-based drawing of SVG files, which can be read and
manipulated in vector graphics programs. You can export any of the
Twine "Views", then manipulate color, size, layers, elements, etc.
to make pretty figures. You can save the current analysis,
so you can work on it later. You can save motifs into libraries to
organize your thinking. You can also export all matches, if you
just need a printout of where each motif is found. Finally,
AlignedSequences can be sent to other Java programs via the
Java Simple Plugin Framework, manipulated, then returned to be
displayed in Twine.
- SVG (Scalable Vector
Graphics) of graphical representations
- Compatible with Web Browsers, Adobe Illustrator, Inkscape
- Independently manipulate each element
- This was made possible by the Batik Java
library for creating SVG files.
- Save the current analysis (alignments and motifs)
- Save motif libraries
- Export sub-sequences as FASTA alignments based on graphical
selection
- Export all matches
(tab-delimited)
- Export to user-written plugins
using Java Simple
Plugin Format (JSPF)