How do I format from a template?
If the primary sequence of a rna strand is in register with other strands in an
alignment file and the secondary structure graph exists for the rna strand,
then a secondary structure graph can be produced for any other strand
in that alignment file. Currently only "mase" format and "genbank" format are supported
for alignment files. The newly generated secondary structure graph will have
all helices reformated in place including reformatting any hairpin loops.
Any extra nucleotides in the new secondary structure graph belong in connecting
loops to be further edited. They will be placed in the upper right hand
corner of the new secondary structure graph in contiguous sets of nucleotides.
This is done in case there is complicated positioning of single stranded
nucleotides in the parent secondary structure graph that needs to be maintained.
The steps for producing a new secondary structure graph from a template are:
- Start up XRNA and go to the "Format" panel. Select the "Derive structure
from template" button.
- Read in an alignment file (currently only "*.mase" files or "*.gb"
files).
- Select a template name and the new name to be derived. Currently the
template name must match the prefix name to a "*.xrna" file.
- Press the "Preview Template" button to view the XRNA I/O file that contains
the rna strand that will act as the template. If the XRNA I/O file contains more
than one rna strand then select the name of the strand in the "Pick Strand" button
in the "Main Controls" panel. The name of the rna strand in the XRNA I/O file
must match the template name in the alignment file. If need be, change the name of the
rna strand using the "rna strand" properties menu while in the "Edit" tab.
- Select the "Run Derive" button. This will generate a new
XRNA I/O file on your disk for the new structure (the new name with the ".xrna" extension).
The derived secondary structure graph will appear as an image in a frame for preview.
Select the "Run Derive" button as often as needed with any new options selected.
The new xrna file will be updated accordingly. The color code for the newly derived
structure is
- red means there is a nuc in the new structure that exactly matches
the nuc in the parent structure
- blue means that there is a nuc in the child structure
and a nuc in the parent structure
- black is for extra nucs in the child structure
- blank areas mean that there are no corresponding nucs in the
child structure for nucs in the parent structure.
- When finished deriving the new structure, note the name of the new structure,
close the "Derive structure" menu. Select the Import/Export tab and open up the
newly derived structure for further editing. Further editing usually starts with
dealing with extra nucs that are in the upper right hand corner of the figure.
These will always be black and placed in rows with contiguous nuc numbering.
These extra nucs almost certainly belong to connecting loop regions. The easiest
way to deal with these rows of extra nucs is by doing the following:
- first get into the "Edit" panel
- select the "rna single strand" constraint mode
- right mouse click on any extra nuc in a row
- when the edit properties menu appears for the single strand then
select the button that says "Readjust Arc to default" in the "Format Arced:"
subpanel. This will cause the nucs in a row to disappear from the row and
reappear in their proper area.
Type at a command line window:
java -jar xrna.jar -derive template_name derived_name alignment_file
Where template_name is the name of the sequence in an alignment file acting as a template.
Where derived_name is the name of the sequence in an alignment file to be derived.
Where align_file is the name of the alignment file in mase or Genbank format
Currently an alignment file must have the extension '.mase' for a mase alignment file or '.gb'
for a Genbank alignment file.
For example:
java -jar xrna.jar -derive e.coli_5s thermus.5s 5s.align.mase
will generate a XRNA input file called thermus.5s.xrna derived from a XRNA input file called
e.coli_5s.xrna given that there are the 2 sequences called e.coli_5s and thermus.5s in
the alignment file called 5s.align.mase. The primary structure in e.coli_5s.xrna must
match the primary structure in 5s.align.mase under the name e.coli_5s.