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George M. Church Laboratory

Analysis Software 

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 


Software Tools

AlignACE

AlignACE (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.
 

ScanACE

ScanACE (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.

README

Click here for descriptions of program output and other information.

HARVARD UNIVERSITY END-USER LICENSE AGREEMENT

AlignACE ("The Program")

GENERAL STATEMENT.

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.

OWNERSHIP OF PROGRAM.

The Program is protected by copyright laws and foreign treaties, and is the subject of a United States patent application, all foreign rights protected. All title, ownership rights, and intellectual property rights in The Program shall remain in Presiden t and Fellows of Harvard College.

GRANT OF RIGHTS.

President and Fellows of Harvard College (hereinafter "HARVARD," "our") grants to LICENSEE (hereinafter "LICENSEE," "you," "your") a non-exclusive license to use The Program free of charge if (a) you are a student, faculty member or staff member of an edu cational institution, or an employee of an organization which meets HARVARD's criteria for a charitable, religious, or not-for-profit organization; and (b) your use of The Program is not for (i) the production or manufacture of products for sale, nor (ii) the performance of services for a fee. The Program is provided to you "as is," without any accompanying documentation, services or improvements from HARVARD.

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The license granted by this Agreement will terminate automatically if you fail to comply with the limitations described herein. On termination you must (a) cease all use of The Program and destroy all copies of The Program in your possesion and, (b) ceas e all use of Derivatives and, at HARVARD's election, assign your copyright interests in the Derivatives.

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The Program is provided free of charge on an "AS IS" basis, without warranty of any kind, including without limitation the warranties of merchantability, fitness for a particular purpose and non-infringement. The entire risk as to the quality and perform ance of The Program is borne by you. Should The Program prove defective, you - and not HARVARD - assume the entire cost of any service and repair. The Program is limited in purpose and should be considered experimental. The Program is not fault-toleran t and is not designed or intended for use requiring fail-safe performance in which the failure of The Program could lead directly to death, personal injury, or severe physical or environmental damage ("High Risk Activities"). HARVARD specifically disclai ms any express or implied warranty of fitness for High Risk Activities.

HARVARD MAKES NO REPRESENTATIONS OR WARRANTIES, EXPRESS OR IMPLIED. BY WAY OF EXAMPLE, BUT NOT OF LIMITATION, HARVARD MAKES NO REPRESENTATIONS OR WARRANTIES OF MERCHANTABILITY OR FITNESS FOR ANY PARTICULAR PURPOSE, OR THAT THE USE OF THE PROGRAM WILL NOT INFRINGE ANY THIRD PARTY'S PATENT, COPYRIGHT, OR TRADEMARK. HARVARD DOES NOT WARRANT THAT YOUR USE OF THE PROGRAM WILL BE UNINTERRUPTED OR THAT THE OPERATION OF THE PROGRAM WILL BE ERROR-FREE. YOU AGREE THAT HARVARD OR ANY OF ITS EMPLOYEES, AGENTS, OR CONTRACTORS SHALL NOT BE LIABLE UNDER ANY CLAIM, CHARGE, OR DEMAND, WHETHER IN CONTRACT, TORT, CRIMINAL LAW, OR OTHERWISE, FOR ANY AND ALL LOSS, COST, CHARGE, CLAIM, DEMAND, FEE, EXPENSE, OR DAMAG E OF EVERY NATURE AND KIND ARISING OUT OF, CONNECTED WITH, RESULTING FROM OR SUSTAINED AS A RESULT OF EXECUTING THIS AGREEMENT OR FOR PERFORMING ALL OR ANY PART OF THIS AGREEMENT. IN NO EVENT SHALL HARVARD BE LIABLE FOR SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES, LOSSES, COSTS, CHARGES, CLAIMS, DEMANDS, FEES OR EXPENSES OF ANY NATURE OR KIND. INDEMNIFICATION.

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EXPORT CONTROLS.

None of The Program or underlying information or technology may be downloaded or otherwise exported or re-exported (a) into (or to a national or resident of) Cuba, Iraq, Libya, Yugoslavia, North Korea, Iran, Syria or any other country to which the U.S. ha s embargoed goods or, (b) to anyone on the U.S. Treasury Department's list of Specially Designated Nationals or the U.S. Commerce Department's Table of Denial Orders. By downloading or using The Program, you are agreeing to the foregoing and you are representing and warranting that you are not located in, under the control of, or a national or resident of any such country or on any such list.

MISCELLANEOUS.

If any provision of this Agreement is held to be unenforceable, such provision shall be reformed only to the extent necessary to make it enforceable. This Agreement shall be governed by and interpreted in accordance with Massachusetts law (excluding the conflict of laws rules). The application of the United Nations Convention of Contracts for the International Sale of Goods is expressly excluded. If you and HARVARD have a dispute concerning any aspect of this Agreement, it shall be resolved in the applicable state or federal courts of Massachusetts. You and HARVARD consent to the jurisdiction of such courts and waive any jurisdictional or venue d efenses otherwise available.

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This Agreement represents the complete agreement concerning this grant of license and can only be amended in writing, executed by both you and HARVARD. In order to download The Program, you must click on the "Accept" box, which indicates your acceptance of the terms of this Agreement. (It is recommended that you also print a copy of this Agreement and keep it for your files.)

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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