The MEME Suite

Various MEME Suite programs require as input a file containing genomic loci. These input files must be in BED format, which must be plain text, not WORD, .doc, .docx, .rtf or any other word-processor format.

BED (Browser Extensible Data) format provides a flexible way to define the loci of genomic regions. Below, we give a brief description of BED format, as used by some of the MEME Suite tools. For a more complete definition, please see the original document at UCSC describing the BED Format.

The first three required BED fields are:

1. chrom - The name of the chromosome (e.g. chr3, chrY, chr2_random) or scaffold (e.g. scaffold10671).
2. chromStart - The starting position of the feature in the chromosome or scaffold. The first base in a chromosome is numbered 0.
3. chromEnd - The ending position of the feature in the chromosome or scaffold. The chromEnd base is not included in the display of the feature, however, the number in position format will be represented. For example, the first 100 bases of chromosome 1 are defined as chrom=1, chromStart=0, chromEnd=100, and span the bases numbered 0-99 in our software (not 0-100), but will represent the position notation chr1:1-100.

The 9 additional optional BED fields are:

4. name - Defines the name of the BED line. The MEME Suite tools ignore the contents of this field.
5. score - A score between 0 and 1000.
6. strand - Defines the strand. Either "." (=no strand) or "+" or "-".
7. thickStart - The MEME Suite tools ignore the contents of this field.
8. thickEnd - The MEME Suite tools ignore the contents of this field.
9. itemRgb - The MEME Suite tools ignore the contents of this field.
10. blockCount - The MEME Suite tools ignore the contents of this field.
11. blockSizes - The MEME Suite tools ignore the contents of this field.
12. blockStarts - The MEME Suite tools ignore the contents of this field.