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Processes large DNA data sets. PairMotifChIP is an efficient method for extracting pairs of I-mers. It obtains motifs by combining extracted I-mers based on clustering methods. The tool is able to make motif discovery without any prior information. It may not work well on the traditional promoter sequence data set containing dozens of sequences because of the lack of sufficient motif information.

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PairMotifChIP classification

PairMotifChIP specifications

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Programming languages:
C, C++
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Command line interface
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PairMotifChIP distribution


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PairMotifChIP support


  • Qiang Yu <>


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School of Computer Science and Technology, Xidian University, Xi’an, China; School of Electronic Engineering, Xidian University, Xi’an, China

Funding source(s)

Supported in part by the National Natural Science Foundation of China under Grants 61502366 and 61373044, the China Postdoctoral Science Foundation under Grant 2015M582621, the National Key Research and Development Program of China under Grant 2016YFC0102000, and the Fundamental Research Funds for the Central Universities under Grants JB150306 and XJS15014.

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