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What is K-mer, and what is it used for?  

2014-10-17 04:29:19|  分类: 生物信息编程 |  标签: |举报 |字号 订阅

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K-mer is used for aligning numberous short reads against a genome.

The idea is that algorithm is to align short  fragments of genome that are generated by K-mer method.

That also says we can just align sequenced short reads against K-mer short fragments of genome.

So, if we define 14-mer, there are 415 types of short fragments (each position is consisted either of A/G/C/T, which can be easily located on genome. As long as we know which short fragment  the sequenced shorted read could be matched, then we can quickly know mapping location on genome for the short read.

In fact, most of algorithm loads all of K-mer fragments into memory. So, sometimes, we could set K-mer as 14, 12, 15-mer to build genome library index. Normally, 32-bit machine uses 12-mer and 64-bit machine uses 14-mer. A 15mer index requires 9GB memory to build and run. The advantage is that 15-mer is that it is faster (or comparable) than 14-mer for all alignments. It is much faster for gapped alignment and novel exon junction (essentially deletion).

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