File Formats

AlignACE output files

Each alignACE output file contains a list of the parameters used, the length and names of the input sequences, and a list of up to 15 motif alignments found. For each motif alignment, the data columns are as follows: sequence alignment, input sequence number, start position for the alignment within this input sequence, 1 (forward) or 0 (reverse), an alignment of the active columns only, a similarity score, and the distance upstream of the start of the sequence. The MAP score as well as several additional indices are given for each motif. Click here for more information on AlignACE.


These tab-delimited text files contain one line for each motif with MAP score greater than five. The motifs are ranked in order of increasing site specificity score. Each line contains the following seven columns:

  1. Name of the group used to find the motif. Each name is linked to the AlignACE output file containing the motif. Organism names are abbreviated as follows:
    • Archaeoglobus fulgidus (AG)
    • Aquifex aeolicus (AA)
    • Borrelia burgdorferei (BB)
    • Bacillus subtilis (BS)
    • Chlamydia trachomatis (CT)
    • Escherichia coli K12 (EC)
    • Haemophilus influenzae (HI)
    • Helicobacter pylori (HP)
    • Mycoplasma genitalium (MG)
    • Methanococcus janaschii (MJ)
    • Mycoplasma pneumoniae (MP)
    • Methanobacterium thermoautotrophicum (TH)
    • Mycobacterium tuberculosis (MT)
    • Pyrococcus horokoshii (PH)
    • Ricksettia prowazekii (RP)
    • Synechocystis sp. (CY)
    • Trepenoma pallidum (TP)
    Group names are assigned as follows:
    • groups derived from conserved operons: a 3-digit number (e.g. 001)
    • groups derived from known E. coli regulons: the name of the E. coli DNA-binding protein (e.g. argR)
    • KEGG functional groups: a 5-digit number (e.g. 00010)
  2. Motif number within the AlignACE output file
  3. Known E. coli motifs similar to this motif (CompareACE > 0.7)
  4. MAP score
  5. Site specificity score
  6. Palindromicity

Abigail Manson McGuire
Genetics Department
Harvard Medical School/BCMP
200 Longwood Ave.
Boston, MA. 02115.
Telephone: (617) 432-4136