General Technique

Mogul is a software tool that integrates more than 30 off-the-shelf computational algorithms that identify putative transcription factor binding sites (TFBS) in undecorated DNA sequence(s). The code framework is written in Perl, providing unified methods to run the algorithms and to report results in a common format (GFF), such that they can later be integrated and visualized. Results can be visualized using various external genome browsers such as Apollo and Argo.

Mogul can be used in a number of ways:

1. Web UI (user interface): Users can interactively select the algorithms that they wish to use, allowing different combinations of analyses to be run. The interface is a simple click-box design, where results are reported in GFF format, postscript and PDF.
2. Programmatic UI: It is possible to run analyses directly from a command line. This currently allows greater flexibility than the web interface and is useful for run analyses where the parameters of the algorithms can be accessed and modified.
3. Optimization: An on-going project is using optimiZtation techniques to identify sets of algorithm parameters that deliver the most reliable set of putative TFBS predictions.
4. Access to Mogul: Due to various license agreements attached to the various algorithms integrated within Mogul, access to Mogul is currently restricted to internal ISB use only. The intention is to release the Perl framework code in the near future and have external users download the algorithm binaries themselves, thereby having them agree to the specific license agreements that exist.

Current Web page: http://www.motifmogul.org

Purpose/use/application of the technique:

Mogul is used for making putative predictions of transcription factor binding sites (TFBS) on undecorated DNA sequences. The technique can be used under a number of different scenarios:

1. Verification of suspected known TFBS: For a single sequence, it is possible to scan and verify known TFBS using sequence matrices from external sources such as TRANSFAC and JASPAR.
2. Identification of shared TFBS amongst a group of co-regulated genes.
3. Identification of TFBS resulting from the conservation of DNA sequence between the same gene across multiple species.
4. Annotating "virgin" genes: For genomes that have recently been sequenced, and where prior annotation of TFBS is unknown, ab-intio scans using the suite of algorithms can provide initial insights into the potential regulatory regions of genes.

Example(s) of projects at ISB that use this technique:

1. Pointillist: A subset of the algorithms in Mogul was used to generate evidence data for the Pointillist project.
2. TLR (Toll-like Receptor) pathway project: Mogul has been used to identify putative TFBS in gene sequences associated with the TLR signaling pathway.
3. TLR set of annotated genes: In-conjunction with the signaling pathway project, Mogul is being used to report potential TFBS into an in-house database serving as a repository of TLR-related genomic annotations.
4. OptimiZation of algorithm parameters for TFBS predictions: The code framework is being used to reverse-engineer genetic regulatory networks from yeast, drosophila, and humans.

Ongoing area of technology development:

Technology · no.
Continuing software development · yes.

	Related Information
			Contact information: Alistair G Rust