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| Content Provider | IEEE Xplore Digital Library |
|---|---|
| Author | Strnadova, V. Buluc, A. Chapman, J. Gilbert, J.R. Gonzalez, J. Jegelka, S. Rokhsar, D. Oliker, L. |
| Copyright Year | 2014 |
| Description | Author affiliation: EECS Dept., Univ. of California, Berkeley, Berkeley, CA, USA (Gonzalez, J.; Jegelka, S.) || Joint Genome Inst., Lawrence Berkeley Nat. Lab., Berkeley, CA, USA (Chapman, J.; Rokhsar, D.) || Comput. Sci. Dept., Univ. of California, Santa Barbara, Santa Barbara, CA, USA (Strnadova, V.; Gilbert, J.R.) || Comput. Res. Div., Lawrence Berkeley Nat. Lab., Berkeley, CA, USA (Buluc, A.; Oliker, L.) |
| Abstract | High-throughput “next generation” genome sequencing technologies are producing a flood of inexpensive genetic information that is invaluable to genomics research. Sequences of millions of genetic markers are being produced, providing genomics researchers with the opportunity to construct highresolution genetic maps for many complicated genomes. However, the current generation of genetic mapping tools were designed for the small data setting, and are now limited by the prohibitively slow clustering algorithms they employ in the genetic marker-clustering stage. In this work, we present a new approach to genetic mapping based on a fast clustering algorithm that exploits the geometry of the data. Our theoretical and empirical analysis shows that the algorithm can correctly recover linkage groups. Using synthetic and real-world data, including the grand-challenge wheat genome, we demonstrate that our approach can quickly process orders of magnitude more genetic markers than existing tools while retaining - and in some cases even improving - the quality of genetic marker clusters. |
| Starting Page | 3 |
| Ending Page | 10 |
| File Size | 838706 |
| Page Count | 8 |
| File Format | |
| ISBN | 9781479956692 |
| DOI | 10.1109/BIBM.2014.6999119 |
| Language | English |
| Publisher | Institute of Electrical and Electronics Engineers, Inc. (IEEE) |
| Publisher Date | 2014-11-02 |
| Publisher Place | UK |
| Access Restriction | Subscribed |
| Rights Holder | Institute of Electrical and Electronics Engineers, Inc. (IEEE) |
| Subject Keyword | Couplings Sociology Clustering algorithms Genetics Statistics Bioinformatics Biological cells |
| Content Type | Text |
| Resource Type | Article |
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