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

Voichita D. Marinescu, Isaac S. Kohane, Tae Kyung Kim, David A. Harmin, Michael E. Greenberg, Alberto Riva

Research output: Contribution to journalArticle

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Abstract

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 s equence 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.

Original languageEnglish (US)
Pages (from-to)999-1001
Number of pages3
JournalBioinformatics
Volume22
Issue number8
DOIs
Publication statusPublished - Apr 2006

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ASJC Scopus subject areas

  • Clinical Biochemistry
  • Computer Science Applications
  • Computational Theory and Mathematics

Cite this

Marinescu, V. D., Kohane, I. S., Kim, T. K., Harmin, D. A., Greenberg, M. E., & Riva, A. (2006). START: An automated tool for serial analysis of chromatin occupancy data. Bioinformatics, 22(8), 999-1001. https://doi.org/10.1093/bioinformatics/btl062