Kmer-indexer: A Fast K-mer Indexing Program

In our previous work, a k-mer based program named MFEprimer-2.0 was designed and developed for primer specificity evaluation task. In order to increase the index processing speed, decrease the index data size and memory usage, we developed a new program named kmer-indexer. Compared to MFEprimer-2.0,...

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Bibliographic Details
Published in:	Studies in health technology and informatics Vol. 216; p. 1083
Main Authors:	Xiaolei, Wang, Wubin, Qu, Chenggang, Zhang, Dongsheng, Zhao
Format:	Journal Article
Language:	English
Published:	Netherlands 2015
Subjects:	Algorithms Base Sequence Chromosome Mapping - methods Database Management Systems Databases, Genetic DNA - genetics Information Storage and Retrieval - methods Molecular Sequence Data Sequence Alignment - methods Sequence Analysis, DNA - methods Software
Online Access:	Get more information
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Summary:	In our previous work, a k-mer based program named MFEprimer-2.0 was designed and developed for primer specificity evaluation task. In order to increase the index processing speed, decrease the index data size and memory usage, we developed a new program named kmer-indexer. Compared to MFEprimer-2.0, the processing speed of kmer-indexer is 10+ times faster, the index data size can be significantly reduced to one third, and the memory usage is controlled within a small range so that this program can run on an ordinary PC.
ISSN:	0926-9630
DOI:	10.3233/978-1-61499-564-7-1083