alternatives to meme suite

Question

[kws15]

Hi everyone,

i have been doing analysis on promoters and i know meme is a great tool to use, however, i need to study thousands of promoter sequences and it is ok to use meme to get thousands of results, but meme does not provide any tools to analyse and interpret thousands of their output files, for example, the web page and the text files with the motif positions stated.

Therefore, i am looking for any alternatives to meme, i am currently using bioconductor of R, this package called PWMenrich can do motif enrichment analysis, but it does not have a lot of the advantages of meme for example telling me all the motifs positions and the beautiful graphic outputs. it only shows all the motifs for a promoter sequence and rank them according to p value. however, i need something more such as their positions in the promoter regions. Any suggestions would be much appreciated , many thanks

Answer 1

[EagleEye]

Try using Homer motif analysis.

Or check this link for more,

https://omictools.com/motif-discovery-category

Answer 2

[Félix]

There is now a R interface for the MEME suite available here : https://github.com/snystrom/memes

Answer 3

[natasha.sernova]

See this old post, it may help.

Creating Groups Of Similar Dna Motifs