A Gibbs sampling strategy applied to the mapping of ambiguous short-sequence tags.
BACKGROUND
Chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq) is widely used in biological research. ChIP-seq experiments yield many ambiguous tags that can be mapped with equal probability to multiple genomic sites. Such ambiguous tags are typically eliminated from consideration resulting in a potential loss of important biological information.


RESULTS
We have developed a Gibbs sampling-based algorithm for the genomic mapping of ambiguous sequence tags. Our algorithm relies on the local genomic tag context to guide the mapping of ambiguous tags. The Gibbs sampling procedure we use simultaneously maps ambiguous tags and updates the probabilities used to infer correct tag map positions. We show that our algorithm is able to correctly map more ambiguous tags than existing mapping methods. Our approach is also able to uncover mapped genomic sites from highly repetitive sequences that can not be detected based on unique tags alone, including transposable elements, segmental duplications and peri-centromeric regions. This mapping approach should prove to be useful for increasing biological knowledge on the too often neglected repetitive genomic regions.


BACKGROUND
http://esbg.gatech.edu/jordan/software/map


BACKGROUND
king.jordan@biology.gatech.edu


BACKGROUND
Supplementary data are available at Bioinformatics online.
Wang
Jianrong
J
School of Biology, Georgia Institute of Technology, Atlanta, GA 30332, USA.
Huda
Ahsan
A
Lunyak
Victoria V
VV
Jordan
I King
IK
D000465:Algorithms; D001483:Base Sequence; D047369:Chromatin Immunoprecipitation; D019295:Computational Biology / Q000379:methods*; D004251:DNA Transposable Elements / Q000235:genetics; D016678:Genome; D017422:Sequence Analysis, DNA / Q000379:methods*; D016324:Sequence Tagged Sites
D004251:DNA Transposable Elements