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Nucleic Acids Research, 2002, Vol. 30, No. 21 e121
© 2002 Oxford University Press

EZ-Retrieve: a web-server for batch retrieval of coordinate-specified human DNA sequences and underscoring putative transcription factor-binding sites

Haibo Zhang1,2, Y. Ramanathan1, Patricia Soteropoulos1,3, Michael L. Recce1,2 and Peter P. Tolias*,1,3

1 Center for Applied Genomics, Public Health Research Institute, 225 Warren Street, ICPH W420M, Newark, NJ 07103, USA, 2 Center for Computational Biology and Bioengineering, New Jersey Institute of Technology, NJ 07102, USA and 3 Department of Microbiology and Molecular Genetics, UMDNJ-New Jersey Medical School, Newark, NJ 07103, USA

*To whom correspondence should be addressed at Center for Applied Genomics, Public Health Research Institute, 225 Warren Street, ICPH W420M, Newark, NJ 07103, USA. Tel: +1 973 854 3450; Fax: +1 973 854 3453; Email: tolias{at}phri.org

The availability of a draft human genome sequence and ability to monitor the transcription of thousands of genes with DNA microarrays has necessitated the need for new computational tools that can analyze cis-regulatory elements controlling genes that display similar expression patterns. We have developed a tool designated EZ-Retrieve that can: (i) retrieve any particular region of human genome sequence from the NCBI database and (ii) analyze retrieved sequences for putative transcription factor-binding sites (TFBSs) as they appear on the TRANSFAC database. The tool is web-based, user-friendly and offers both batch sequence retrieval and batch TFBS prediction. A major application of EZ-Retrieve is the analysis of co-expressed genes that are highlighted as expression clusters in DNA microarray experiments.


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