Variant Annotation Public Deposited

http://ir.library.oregonstate.edu/concern/graduate_projects/r494vm32t

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  • With the development of technologies in genome sequencing and variant detection, a huge number of variants are detected. To further analyze the variants, it requires an efficient tool to annotate the functional effect of variants. This project managed to develop an efficient program to annotate the functional effect of variants based the locations of variants. It also proposed two algorithms, an array-based algorithm and a tree-based algorithm, to expedite the searching process. The array-based algorithm is more efficient for sorted variants whereas the tree-based algorithm is more efficient for unsorted variants. Compared with naive searching algorithm, the array-based algorithm reduces the searching complexity from O(NK) to O(N + K) while the tree-based algorithm reduces to O(K log N), where N is the number of genes and K is the number of variants. According to the experiment, the two algorithms succeed in annotating the variants and take less than 1 second to annotate 105 variants whereas naive algorithm takes about 133 seconds.
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  • description.provenance : Approved for entry into archive by Steven Van Tuyl(steve.vantuyl@oregonstate.edu) on 2016-12-29T22:06:19Z (GMT) No. of bitstreams: 2 license_rdf: 1527 bytes, checksum: d4743a92da3ca4b8c256fdf0d7f7680f (MD5) HeJun2016.pdf.pdf: 327344 bytes, checksum: 121de00a4d0b7f42eff0d01e9adc0ca4 (MD5)
  • description.provenance : Made available in DSpace on 2016-12-29T22:06:19Z (GMT). No. of bitstreams: 2 license_rdf: 1527 bytes, checksum: d4743a92da3ca4b8c256fdf0d7f7680f (MD5) HeJun2016.pdf.pdf: 327344 bytes, checksum: 121de00a4d0b7f42eff0d01e9adc0ca4 (MD5) Previous issue date: 2016-12-12
  • description.provenance : Submitted by Jun He (hej2@oregonstate.edu) on 2016-12-23T04:46:21Z No. of bitstreams: 2 license_rdf: 1527 bytes, checksum: d4743a92da3ca4b8c256fdf0d7f7680f (MD5) HeJun2016.pdf.pdf: 327344 bytes, checksum: 121de00a4d0b7f42eff0d01e9adc0ca4 (MD5)

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