George M. Church Laboratory
for mRNA Abundance Data
The purpose of this page is to share software generated by our laboratory for analyzing mRNA abundance data.
At present, this site contains only software developed in the context of a recent article:
Finding DNA Regulatory Motifs within Unaligned Non-Coding Sequences Clustered by Whole-Genome mRNA Quantitation, Roth, F.R., Hughes, J. D., Estep, P. E. & G.M. Church, Nature Biotechnology 1998
Please cite this work when describing results obtained from the software that is offered here
AlignACEAlignACE (Aligns Nucleic Acid Conserved Elements) is a program which finds sequence elements conserved in a set of DNA sequences. It uses a Gibbs sampling strategy which is similar to that described by A. F. Neuwald, J.Liu and C.E. Lawrence in Gibbs motif sampling: Detection of bacterial outer membrane protein repeats An iterative masking procedure is used to allow multiple distinct motifs to be found within a single data set.
ScanACEScanACE (Scans for Nucleic Acid Conserved Elements) is a program which scans DNA sequence for elements which match a DNA motif. It uses a weight matrix approach, with weights assigned by the method of Berg and von Hippel. Given an appropriately formatted feature table such as the ORF table provided by SGD, ScanACE is also able to return information about the genomic environment of each site found.
As of April 25, 1999, both Linux and Win 95/98/NT versions are available. Some new features have been added to ScanACE as well. You may obtain all files necessary for running AlignACE and ScanACE on a Linux or Windows 95/98/NT machine by indicating y our acceptance of our licensing agreement and providing your name and email address below.
If your browser does not prompt you to save the file to disk, use the "Save As" function to save it as either alignace.zip (Windows) or alignace.tar.gz (Linux). Follow customary procedures for each system to extract the archived contents. Sample input files, output files, and support files for the Saccharomyces cerevisiae genome are included.
READMEClick here for descriptions of program output and other information.
HARVARD UNIVERSITY END-USER LICENSE AGREEMENTAlignACE ("The Program")
The Program is a research tool still in the development stage. This license Agreement is entered into in order to encourage scientific collaboration aimed at further development and use of The Program.
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Any commercial use of this or other software can be discussed with the HMS Office of Technology Licensing (OTL) contact Maryanne Fenerjian.
Please direct any other questions or comments to Zhou Zhu.
This page was last modified 03 Sep 99 by JH; 20-aug-1999 GMC