Hi to all!
I'm struggling to learn MEME, and I have a question on it.
I have 6 promoter sequences of one protein from Arabidopsis. I put them in a fasta file and input it to MEME to find out conserved motifs.
Finally, I got a motif from MEME and I thought there might be any functions or roles genetically since they are conserved promoter motif, so I put it on BLASTn but here is a problem.
The motif has other nucleotide symbol, not ATGC but MHW..stuffs so BLAST reject the input file. What I've done afterwards are 2 things.
- I can get exact conserved motif sequence from MEME composed of only ATGC symbol from 6 sequences, so I put the 6 motif sequences into a single fasta file and BLAST them at once. File looks like this. > motif seq from LOC_1 ATCGCGCTAGTCT > motif seq from LOC_2 CTCGTAGTAGCT > motif seq from LOC_3
And I got many results from BLAST saying many functions on each sequence.
- I put the 6 motif sequences into AME on MEME using JASPAR Redundant database since I'd like to know their functions among all capable species on database. It's been running so far so I don't know whether what I'm doing is right or not......
If there another better way to find out function of motif, please let me know...