Thesis Advisor: George M. Church, Ph.D.
Harvard Medical School, Dept. of Genetics
last updated: March 2001
This package is designed for the analysis of Affymetrix E. coli oligonucleotide arrays as described in Selinger et al, Nature Biotechnology18:1262-8 (2000). It can be used in conjunction with Affymetrix's GeneChip© software package and extends its functionality in several ways:
- More flexibility in the way the analysis is done
- An algorithm which corrects for varying signal in different regions of the chip
- High resolution analysis, allowing data to be analyzed oligo by oligo
- Handles replicates and multiple timepoints
- Automatic annotation of results
- All output files can easily be opened and analyzed in Excel
- Detection of transcripts is decided by a simple statistical test
We are grateful for the tremendous foresight that Affymetrix has shown in permitting the public release of all of the E. coli array oligo sequences. This has allowed expression to be monitored at an unprecedented resolution, with on average one probe every 30 bases throughout the entire genome. We feel that high resolution expression profiling is the logical next step in the evolution of high density DNA array experiments and we thank Affymetrix for making it possible.
GAPS© is a set of Perl scripts which will run on all platforms for which Perl is available (Windows, Macintosh, Linux, Unix, etc.). Perl is run-time compiled and is therefore open source by definition. We welcome modifications and improvements to the code.
Download GAPS© (zipped - 4.7 MB) NOTE: this package contains oligo sequence files in the "ref" folder.
GAPS© updates page. Important fix for GAPS© version 1-1 (Ignore this if you're downloading for the first time.)
Download just the GAPS© manual (Adobe© PDF format - 694KB)
Download E. coli array oligo files
Download high resolution
files from Selinger et al (2000)
This page has been accessed at least times since the counter was last reset on April 16, 2001,
at an average rate of about
hits per day.