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| Content Provider | IEEE Xplore Digital Library |
|---|---|
| Author | Qiang Yu Hongwei Huo Vitter, J.S. Jun Huan Nekrich, Y. |
| Copyright Year | 2013 |
| Description | Author affiliation: Inf. & Telecommun. Technol. Center, Univ. of Kansas, Lawrence, KS, USA (Vitter, J.S.; Jun Huan; Nekrich, Y.) || Sch. of Comput. Sci. & Technol., Xidian Univ., Xi'an, China (Qiang Yu; Hongwei Huo) |
| Abstract | Motif stem search (MSS) is a recent motif search problem to search motifs on large-alphabet inputs. A motif stem is an l-length string with some wildcards. The goal of the MSS problem is to find a set of stems that represents a superset of all (l, d) motifs present in the input sequences. The three main contributions of this paper are as follows: (1) We build motif stem representation more precisely by using regular expressions. (2) We give a new method for generating all possible motif stems. (3) We propose an efficient algorithm, called StemFinder, for solving the MSS problem. Compared with the previous algorithms, StemFinder runs much faster and first solves the (17, 8), (19, 9) and (21, 10) challenging instances on protein sequences; moreover, StemFinder reports fewer stems representing a smaller superset of all (l, d) motifs. |
| Sponsorship | IEEE Comput.Soc. |
| Starting Page | 473 |
| Ending Page | 476 |
| File Size | 477754 |
| Page Count | 4 |
| File Format | |
| ISBN | 9781479913091 |
| DOI | 10.1109/BIBM.2013.6732539 |
| Language | English |
| Publisher | Institute of Electrical and Electronics Engineers, Inc. (IEEE) |
| Publisher Date | 2013-12-18 |
| Publisher Place | China |
| Access Restriction | Subscribed |
| Rights Holder | Institute of Electrical and Electronics Engineers, Inc. (IEEE) |
| Subject Keyword | Algorithm design and analysis exact algorithms Radiation detectors DNA regular expressions Search problems Silicon Planted motif search motif stem search Bioinformatics Time complexity |
| Content Type | Text |
| Resource Type | Article |
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