Examples for AlignACE

This example runs AlignACE on a file containing sequences upstream of a number of galactose utilization genes in Saccharomyces cerevisiae.

Example files include:

• GAL.seq, the input file.
• alignace.sh, the job script.
• alignace.out, standard error and output.

The output file contains a list of the names of the input sequences. The numbers associated with these names are used in the subsequent motif descriptions to refer to the input sequences. Motifs are then listed in order of descending MAP score, the metric for motif strength used by AlignACE.

The fields in AlignACE output following Motif x are:

1: site sequence (*'s below indicate 'active' motif columns)

2: number of the sequence from which the site was found (listed at the top of the output file)

3: position of the site in that sequence (specifically, the position of the site column nearest the beginning of the input sequence)

4: strand (1=forward, 0=reverse)

As mentioned above, the *'s indicate active columns.