Greetings, I've been trying to replicate results from the following research article: https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-018-2378-9 In the paper, there is a figure that describes motif #57 with a sequence logo and its position weight matrix.
I took the data from the given datasets in additional material section and gathered the FASTA files needed to process through MEME.
The combined dataset(denoted CM in the paper) was processed through MEME but I obtained different motifs than those obtained by the authors. I checked the datasets and my FASTA files and they are correct, I'm unsure of how this discrepancy between my results and theirs exists, as I followed the paper.
I suspect that maybe the FASTA files changed over a year in the Uniprot database since the paper is from 2018 and we are in 2019. I searched in MEME for motifs with length 3 to 10, as this describes the motifs discussed in the paper.
Any thoughts or possible directions?
Here is the Motif they are showing: (57)
Here is the motif I got: