Centrimo output as input for Spamo

[Mike]

Can I use the motifs found and output by centrimo as the input for spamo, like you can do with the output from meme? The centrimo output .txt and .html files don't work and there doesn't seem to be an appropriate conversion script. Or does it not make sense to use centrimo output as spamo input?

[CharlesEGrant]

Hi Mike,

The output of Centrimo is really just a list of the names of motifs identified as being enriched in the central region of the sequence data. The Centrimo output doesn't contain the detailed data for the motifs so it can't be used as the input for Spamo. Notice though that one of the inputs you provided to Centrimo is a motif file. That's where all the detailed motif information resides. You could use the same motif file you submitted to Centrimo as one of the inputs to Spamo.

Note that you have to provide Spamo with at least two motifs: the primary motif, and one or more secondary motifs. For the command line version of Spamo there are several options that let you select which motifs within a file you want to use a the primary.  By default all the other motifs in a file will be considered as secondaries. The web application is not as flexible. Please check the Spamo documentation for more details.

You may also want to look at meme2meme, one of the command line utilities distributed with the MEME Suite source. This will let you extract selected motifs from one file and save them to another. This can be useful if you want to narrow down the collection of motifs considered as secondaries.

Charles