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PRE Mapper
PRE Mapper is a bioinformatic tool written in Perl for searching Polycomb Response Elements (PREs) in Drosophila. This tool's algorithm uses motif of PRE binding proteins and looks for motif clusters and patterns to define a PRE.

The motifs used in this tool include Pho, GAF, Dsp1, Sp1, Zeste, Grh, Adf1 and Cg. For additional information about these motifs and binding proteins, please click here.

PRE motif clusters & conditions for PRE search
  • Pho-distinct cluster (Pho, GAF, DSP1, Zeste, Sp1 motifs) & Total Motifs 10 & Average Gap 60.
  • Pho-generic cluster (Pho + four other motifs) & Total Motifs 16 & Average Gap 40.
  • Cg or Pho-independent cluster (two Cg motifs + four other motifs)& Total Motifs 16 & Average Gap 40.
Any given PRE may possess at least one of the above clusters on it.

The Drosophila Data:
The result of PRE search using this PRE Mapper tool is provided in the below table, as bed formatted files:
  Release 4 / dm2 Release 5 / dm3 Release 6 / dm3
PRE Mapper PRE List Release4_dm2_PREs.bed Release5_dm3_PREs.bed Release6_dm6_PREs.bed

Download PRE Mapper:
Currently, the PRE Mapper tool is available as a command line Perl script for download and requires Perl alone to run on any computer. It takes FASTA formatted sequence file as input and produces different text output files.

Please click here to download the PRE Mapper tool.

If you have any queries regarding installation or running the tool please contact asrini@ccmb.res.in

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