AlignACE Homepage

Software Download

You may download AlignACE here.

Accessory programs can be downloaded here.

Online Services

Extraction of upstream regions in Saccharomyces cerevisiae for the purposes of motif finding.

AlignACE motif-finding algorithm.

CompareACE to selected motifs in Saccharomyces cerevisiae.

Full Analysis of upstream regions of selected genes in Saccharomyces cerevisiae. This is a unification of the three previous services. Specificity scores are also given. Computational resources are limited, so restrictions are placed on the amount of sequence that may be searched by AlignACE, as well as on the number of allowed simultaneous users.


Computational identification of cis-regulatory elements associated with groups of functionally related genes in Saccharomyces cerevisiae, Hughes, JD, Estep, PW, Tavazoie S, & GM Church, Journal of Molecular Biology 2000 Mar 10;296(5):1205-14.

Finding DNA Regulatory Motifs within Unaligned Non-Coding Sequences Clustered by Whole-Genome mRNA Quantitation, Roth, FR, Hughes, JD, Estep, PE & GM Church, Nature Biotechnology 1998 Oct;16(10):939-45.

Results for Saccharomyces cerevisiae

Groups analyzed and AlignACE results for Hughes, et al, paper.

mRNA abundance data for heat shock, galactose induction, and mating type comparisons from the Roth, et al, paper.

Other useful websites

Church Lab Homepage





Please address questions or comments to Jason D. Hughes at

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