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Bioinformatics Advance Access originally published online on February 24, 2006
Bioinformatics 2006 22(8):999-1001; doi:10.1093/bioinformatics/btl062
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© The Author 2006. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

START: an automated tool for serial analysis of chromatin occupancy data

Voichita D. Marinescu 1,*, Isaac S. Kohane 1, Tae-Kyung Kim 2, David A. Harmin 2, Michael E. Greenberg 2 and Alberto Riva 1,{dagger}

1 Children's Hospital Informatics Program at the Harvard-MIT Division of Health Sciences and Technology, Harvard Medical School 300 Longwood Avenue, Boston, MA 02115, USA
2 Division of Neuroscience, Children's Hospital Boston, Harvard Medical School 300 Longwood Avenue, Boston, MA 02115, USA

*To whom correspondence should be addressed.

Summary: The serial analysis of chromatin occupancy technique (SACO) promises to become a widely used method for the unbiased genome-wide experimental identification of loci bound by a transcription factor of interest. We describe the first web-based automatic tool, termed sequence tag analysis and reporting tool (START), for processing SACO data generated by experiments performed for the yeast, fruit fly, mouse, rat or human genomes. The program uses as input sequences of inserts from a SACO library from which it extracts all SACO tags, maps them to genomic locations and annotates them. START returns detailed information about these tags including the genes, the genomic elements and the miRNA precursors found in their vicinity, and makes use of the MAPPER database to identify putative transcription factor binding sites located close to the tags.

Availability: The program is available at http://bio.chip.org/start/

Contact: vdmarinescu{at}chip.org

Supplementary information: Supplementary information is available at http://bio.chip.org/doc/start/START-supplementary.pdf

Received on December 19, 2005; revised on February 15, 2006; accepted on February 18, 2006

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