Research Project
Grant-in-Aid for Scientific Research (C)
I constructed genome assemblies with the whole genome sequencing reads from budding yeast, nematoda, and rice, and determined the statistics for the metrics and error properties of the assemblies. Using the likelihood ratio of the alignment properties (i.e., alignment length, alignment identity, and mapping rate of paired-end short reads) between the true and false alignment data, I developed a gap-closing tool, GMcloser, that closes gaps in assemblies with high accuracy. In addition, I developed another too tools, GMvalue and Extrerm. GMvalue determines the metrics of misassemblies including the number of misassembles. Extreme reassembles a preassembled config set by extending the termini of the contigs followed by assembling the extended contigs with overlap-layout-consensus algorithm.
All 2017 2016 2015 2014
All Journal Article (8 results) (of which Int'l Joint Research: 1 results, Peer Reviewed: 8 results, Open Access: 8 results, Acknowledgement Compliant: 3 results) Presentation (2 results)
生化学
Volume: 88 Issue: 1 Pages: 44-53
10.14952/SEIKAGAKU.2016.880044
BMC Genomics
Volume: 17 Issue: 1 Pages: 370-370
10.1186/s12864-016-2690-6
120005817905
DNA Research
Volume: 23 Issue: 2 Pages: 171-180
10.1093/dnares/dsw006
Volume: 88 Pages: 44-53
Bioinformatics
Volume: 31 Issue: 23 Pages: 3133-3141
10.1093/bioinformatics/btv465
Nature Biotechnology
Volume: 33 Issue: 5 Pages: 445-449
10.1038/nbt.3188
Nature Genetics
Volume: 47 Issue: 4 Pages: 405-409
10.1038/ng.3241
Plos Computational Biology
Volume: 18 Issue: 9 Pages: e1003841-e1003841
10.1371/journal.pcbi.1003841