One method of investigating gene regulation is to produce a minimal tiling path using overlapping PCR products spotted on a microarray, and hybridising labelled probes enriched by ChIP to look for potential binding sites.
While designing primers and amplicons for small projects of a few kilobases is relatively straightforward, the process becomes prohibitively time consuming with larger tiles of a few megabases or more. To this end we have produced MAMMOT, a set of scripts and visualisation tools for the production of genomic DNA tile arrays. The first part of the toolset uses Perl scripts to break up the sequence into a specified size (typically 1kb segments) and to automatically design minimally overlapping primers in batch using Primer3. MAMMOT will also work on RepeatMasker masked files to avoid large stretches of repetitive sequences and will undergo multiple rounds of primer design to minimise gaps in the tiling path. Results are formatted as a tab-delimited file which can be easily be imported into the mySQL database. A set of PHP scripts then takes the data from the database and provides an easy to navigate web interface showing a tiling diagram in a specified range. Clicking on a PCR tile brings up information about the amplicon including primers, repeat regions and Blastn matches.
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