The preferred sequence format for MEME is Pearson/Fasta format. MEME uses the first word in the title line of each sequence, truncated to 24 characters if necessary, as the name of the sequence. This name must be unique. Sequences with duplicate names will be flagged and ignored. (The first word in the title line is everything up to the first blank following the ">" at the beginning of the line.) MEME accepts protein and DNA sequences in any of the following formats by converting them to Pearson/Fasta format:
MEME uses the ReadSeq program to read in sequences. ReadSeq is copyright 1990 by D. G. Gilbert, Biology Dept., Indiana University.