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Alejandro Barrera
Dec 1, 2015, 4:51:34 PM12/1/15
to MEME Suite Q&A
Hi,
I'm having troubles with the online version of TomTom querying a motif against the RNA database from Ray et al. 2013. When I try to submit the job I get a javascript alert:
The target motifs uses the RNA alphabet but to be compatibile with other inputs it should be DNA.
I'm going to download the latest meme suite and run it locally, but I wanted to give you a heads up on the web issue.
Alex
James Johnson
Dec 3, 2015, 5:49:56 AM12/3/15
to MEME Suite Q&A
The problem is that we upgraded our conversion scripts in preparation for the next release (4.11.0) which has proper support for RNA motifs as a distinct type from DNA motifs (it also supports custom alphabets). The 4.11.0 release was intended to go out early this week but a number of bugs were found last Friday delaying the release. Obviously the motif databases got updated with using the new conversion scripts...
Until this is fixed (or the 4.11.0 release is out) you can download the motif databases and edit any that have "ALPHABET= ACGU" to "ALPHABET= ACGT", then just upload them to the website as a file for the target databases.
Until this is fixed (or the 4.11.0 release is out) you can download the motif databases and edit any that have "ALPHABET= ACGU" to "ALPHABET= ACGT", then just upload them to the website as a file for the target databases.
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