reposting as plain text (sorry about the butt-ugly html in original post):
I'm posting this as a heads up / FYI -- if you want to align RNA sequences with
Mauve, you'll need to edit the sequences first, changing Us to Ts. I couldn't
find it mentioned explicitly anywhere in the documentation or publications --
maybe the description as a DNA genome alignment tool should have clued me in --
but if you use Mauve to align RNA sequences, all of the U residues are stripped
from the sequence(s). An alignment is produced, but it is based on the
sequences sans all U residues. The console does indicate an error reading the
file, but it is akin to the error when annotations are malformed; all of the
output files are generated, and the alignment can be viewed.
...
Completed without error.
Error reading file.
org.biojava.bio.BioException: Could not read sequence
at
org.biojava.bio.seq.io.StreamReader.nextSequence(StreamReader.java:108)
at org.gel.mauve.format.BaseFormat$2.nextSequence(Unknown Source)
at org.gel.mauve.GenomeBuilder.buildGenome(Unknown Source)
at org.gel.mauve.GenomeBuilder.buildGenome(Unknown Source)
at org.gel.mauve.GenomeBuilder.buildGenome(Unknown Source)
at org.gel.mauve.XmfaViewerModel.init(Unknown Source)
at org.gel.mauve.XmfaViewerModel.<init>(Unknown Source)
at org.gel.mauve.ModelBuilder.buildModel(Unknown Source)
at org.gel.mauve.gui.FrameLoader.loadFile(Unknown Source)
at org.gel.mauve.gui.FrameLoader.run(Unknown Source)
at java.lang.Thread.run(Thread.java:680)
Caused by: org.biojava.bio.symbol.IllegalSymbolException: This tokenization
doesn't contain character: 'U'
at
org.biojava.bio.seq.io.CharacterTokenization.parseTokenChar(CharacterTokenization.java:175)
at
org.biojava.bio.seq.io.CharacterTokenization$TPStreamParser.characters(CharacterTokenization.java:246)
at
org.biojava.bio.seq.io.FastaFormat.readSequenceData(FastaFormat.java:188)
at org.biojava.bio.seq.io.FastaFormat.readSequence(FastaFormat.java:153)
at
org.biojava.bio.seq.io.StreamReader.nextSequence(StreamReader.java:105)
... 10 more
** (Image of alignment not attached to this repost). **
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