Hello helene, helene chiapello wrote: > Hi Aaron > I got a question concerning the XMFA format. > I'm trying to extract the aligned sequences corresponding to matches (in > lower case) from > this format and I realize that insertions located between two matches > are also indicated > in lower case. This makes the parsing really complicate because it is > not possible > to identify automatically matches from the XMFA file (the number of > 'lower cases' > blocks is not the same in all the aligned genomes). Don't you think that > the insertions > have to be written in upper case ? Or do you have any other suggestion ? > Hope my question is clear, but I'm not sure... > Thanks > Helene > > Here is an example of an insertion lcated between two matches: >
As far as I am aware, progressiveMauve is case-agnostic. When writing the XMFA output, mauveAligner and progressiveMauve should preserve the upper/lowercase patterns present in the input sequence files. Such behaviour should be useful, since other programs like repeat masking software often use upper/lowercase mixtures to encode the positions of repeats. It's true that parsing an XMFA file is somewhat more complicated than parsing a standard FastA. One good quality is that the XMFA file can be split on = signs and each piece becomes a standard FastA. But perhaps I'm not understanding your question? Is it the sequences which correspond to insertions that you would like to extract from the XMFA? The coordinates of such sequences are encoded in the .backbone and/or .bbcols files generated by progressiveMauve, but to get the sequences one would have to cross-reference one of those files with the XMFA. Regards, -aaron ------------------------------------------------------------------------- This SF.net email is sponsored by the 2008 JavaOne(SM) Conference Don't miss this year's exciting event. There's still time to save $100. Use priority code J8TL2D2. http://ad.doubleclick.net/clk;198757673;13503038;p?http://java.sun.com/javaone _______________________________________________ Mauve-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/mauve-users
