Skip Navigation



Bioinformatics Advance Access published online on February 24, 2006
Bioinformatics, doi:10.1093/bioinformatics/btl062
This Article
Right arrow Advance Access manuscript (PDF) Freely available
Right arrow Supplementary Data
Right arrow All Versions of this Article:
22/8/999    most recent
btl062v1
Right arrow Comments: Submit a response
Right arrow Alert me when this article is cited
Right arrow Alert me when Comments are posted
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Right arrowRequest Permissions
Google Scholar
Right arrow Articles by Marinescu, V. D.
Right arrow Articles by Riva, A.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Marinescu, V. D.
Right arrow Articles by Riva, A.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

© The Author (2006). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org
Received December 19, 2005
Revised February 15, 2006
Accepted February 18, 2006

Applications note

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

1 Children's Hospital Informatics Program at the Harvard-MIT Division of Health Sciences and Technology, Children's Hospital Boston, 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.
Voichita D. Marinescu, E-mail: vdmarinescu{at}chip.org


  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, named START--Sequence Tag Analysis and Reporting Tool, 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/.

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

Associate Editor: Martin Bishop
Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?


This article has been cited by other articles:


Home page
 Genome ResHome page
A. A. Bhinge, J. Kim, G. M. Euskirchen, M. Snyder, and V. R. Iyer
Mapping the chromosomal targets of STAT1 by Sequence Tag Analysis of Genomic Enrichment (STAGE)
Genome Res., June 1, 2007; 17(6): 910 - 916.
[Abstract] [Full Text] [PDF]

Home page
 Am. J. Physiol. Lung Cell. Mol. Physiol.Home page
J. B. Vos, N. A. Datson, K. F. Rabe, and P. S. Hiemstra
Exploring host-pathogen interactions at the epithelial surface: application of transcriptomics in lung biology
Am J Physiol Lung Cell Mol Physiol, February 1, 2007; 292(2): L367 - L377.
[Abstract] [Full Text] [PDF]


Disclaimer: Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.