Promoter Analysis

Information

Use MEME program to identify motifs in the gene's upstream and downstream sequence of determined length.

MEME-Suite: Timothy L. Bailey, Mikael Bodén, Fabian A. Buske, Martin Frith, Charles E. Grant, Luca Clementi, Jingyuan Ren, Wilfred W. Li, William S. Noble, "MEME SUITE: tools for motif discovery and searching", Nucleic Acids Research, 37:W202-W208, 2009. [full text]

Promoter sequence preparation

Input files are Maize genome sequence in FASTA format and gene annotation file in GFF format.
Using the gene start position and end position, obtain the upstream and downstream sequences of length 500 bp, 1k bp, 2k bp, 5k bp, 10k bp. If there is a gene within the sequence, then the sequence is truncated at the start of neighboring gene.

Instructions

Steps to follow

Click on Example set of gene ids. to populate the box with example set of gene ids
OR type in the desired list of gene ids in the box with one gene id per line.
Select the required length of the sequences upsstream and downstream from the dropdown menu
Click on Get Promoter Region to retrieve the sequences.
Wait for the page to load the promoter sequences in tabular format, along with the gene id, gene description, gene position and indicating the upstream and downstream
Select the genes to do Motif discovery using MEME Suite by clicking on Get Motifs
Wait for the appearance of a button called Meme Output and click it to access the MEME results HTML page.

Filter by Experiments:

Example set of gene ids.

Retrieve upstream and downstream

Sequences of length