Motif altered after aligned?

[Gus Dunn]

I THINK I might have found a strange bug. I was dividing a group of
motifs into groups based on sequence similarity by aligning all the
motifs then highlighting a subset that were similar and separating
them from the group as a whole by running a new alignment on just the
selected motifs.

I would then re-align the motifs that were left by doing an alignment
on the inverse of the selected motifs I used above.

However I noticed that after doing a new alignment one of the motifs
has had it sequence change. Specifically it has had a deletion.

This is illustrated by a screen shot i took (http://bit.ly/dsanyl).
You can see that the names of the two motifs in the different windows
are the same but one is missing a 'T'


Anyone else had this happen?

[Matias Piipari]

Hi Gus

Thanks for pointing that out. The default parameter for the nmalign program that does the alignment is to drop all columns that are not supported by at least one column in the alignment (you can change it by running nmalign on the commandline with the parameter -minCols 1). This should really be made a configurable parameter in the preferences (and probably should default to 1 rather than 2 as is done right now).
I've noted this as an issue in the issue tracker here: http://github.com/mz2/iMotifs/issues#issue/17

Will fix this hopefully for next week -- please remind next week if there's no update out!

For now, here's a workaround that allows you to do the motif multiple alignment on the commandline:
/Applications/iMotifs.app/Contents/Resources/Java/nmica-extra/bin/nmalign input.xms -minCols 1 -outputType all > output.xms

Best wishes
Matias

Matias Piipari
- - - - - - - - - - -
http://twitter.com/mz2
http://www.thecosmokid.com