High-throughput expression profiling technologies have led to the possibility of a global understanding of gene regulation in a wide variety of biological systems. Here, I will present the MARSMotif suite of tools based on regression splines, which facilitate discovery of cis-regulatory logic from microarray data. MARSMotif proceeds by correlating cis-regulatory motif occurrences and binding strengths with the gene expression levels using MARS (multivariate adpative regression splines), and identifies functional motif combinations and their associated target genes. These methods do not require gene-clustering and have proven very effective in both lower eukaryotes and mammals. Multiple aspects of transcription regulation, including condition-specific regulation by a common transcription factor, can also be addressed within this framework.

References
1. Das D, Nahlé Z & Zhang MQ. Adaptively inferring human transcriptional subnetworks. Molecular Systems Biology (Nature) (In press)
2. Smith AD, Sumazin P, Das D & Zhang MQ (2005) Mining ChIP-chip data for transcription factor and cofactor binding sites. Bioinformatics 21(Suppl 1): i403-i412 (ISMB 2005)
3. Das D, Banerjee N & Zhang MQ (2004) Interacting models of cooperative gene regulation. Proc Natl Acad Sci U S A. 101: 16234-16239

AMOS - a modular framework for genome assembly and analysis

Mihai Pop
Center for Bioinformatics and Computational Biology, University of Maryland

The AMOS project encompasses modules, software libraries, and tools for generating, analyzing and validating genome assemblies. Converters allow the integration of AMOS with the most widely used genome assemblers. This demo will provide an overview of the main AMOS modules with a special emphasis on AMOScmp – a comparative assembler; minimus – a streamlined assembler for small data-sets; and several tools for assembly validation, including the Assembly Investigator – a visualization tool for the manual inspection of assemblies. We will also describe the integration of AMOS with the NCBI Trace and Assembly archives, and with assembly data in the commonly used .ACE format.

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