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, 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.
Institute of Health Service and Medical Information, Academy of Military Medical Sciences, Beijing, China.
Wang
W
Xiaolei
Beijing Institute of Radiation Medicine, State Key Laboratory of Proteomics, Beijing, China.
Qu
Q
Wubin
Beijing Institute of Radiation Medicine, State Key Laboratory of Proteomics, Beijing, China.
Zhang
Z
Chenggang
Institute of Health Service and Medical Information, Academy of Military Medical Sciences, Beijing, China.
Zhao
Z
Dongsheng
D000465:Algorithms; D001483:Base Sequence; D002874:Chromosome Mapping / Q000379:methods; D004247:DNA / Q000235:genetics*; D003628:Database Management Systems; D030541:Databases, Genetic; D016247:Information Storage and Retrieval / Q000379:methods; D008969:Molecular Sequence Data; D016415:Sequence Alignment / Q000379:methods*; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software
D004247:DNA