Model-P: a basecalling method for resequencing microarrays of diploid samples.
BACKGROUND
Basecalling is a critical step of the analysis of DNA resequencing microarray data for single nucleotide polymorphism discovery and genotyping. For microarrays hybridized with DNA derived from diploid organisms, basecalling with high accuracy at high call rates is a challenging task. Current methods sometimes do not produce satisfactory results.


RESULTS
We explored using physical models based on the sequences of the probe and the target to predict feature intensities in resequencing microarrays. Based on these intensity-predicting models, a new basecalling method (Model-P), which takes into consideration the expected feature intensities for different potential genotypes, was developed. Model-P is shown to have better performance at high call rates compared with ABACUS, the current state-of-the-art method, on a test dataset and on relatively AT-rich regions.


BACKGROUND
Model-P is available upon request.
Zhan
Yiping
Y
Department of Computer Science, University of Massachusetts, Amherst, MA 01003, USA.
Kulp
David
D
D020856:AT Rich Sequence / Q000235:genetics; D000465:Algorithms; D020137:Base Pair Mismatch / Q000235:genetics*; D003198:Computer Simulation; D015342:DNA Probes / Q000235:genetics*; D004171:Diploidy; D018390:Gene Targeting / Q000379:methods*; D008957:Models, Genetic; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D018401:Sample Size; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software
D015342:DNA Probes