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


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


BACKGROUND
SUPPLEMENTARY INFORMATION is available at http://bio.chip.org/doc/start/START-supplementary.pdf
Marinescu
Voichita D
VD
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. vdmarinescu@chip.org
Kohane
Isaac S
IS
Kim
Tae-Kyung
TK
Harmin
David A
DA
Greenberg
Michael E
ME
Riva
Alberto
A
D001185:Artificial Intelligence; D002843:Chromatin / Q000235:genetics*; D002874:Chromosome Mapping / Q000379:methods*; D003628:Database Management Systems; D030541:Databases, Genetic; D016247:Information Storage and Retrieval / Q000379:methods*; D020407:Internet; D012984:Software; D014157:Transcription Factors / Q000235:genetics; D014584:User-Computer Interface
D002843:Chromatin; D014157:Transcription Factors