essaMEM: finding maximal exact matches using enhanced sparse suffix arrays
essaMEM: finding maximal exact matches using enhanced sparse suffix arrays
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DOI：
10.1093/bioinformatics/btt042
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发表时间：
2013-03-15
期刊：
影响因子：
5.8
通讯作者：
Dawyndt, Peter
中科院分区：
文献类型：
--
作者：
Vyverman, Michael;De Baets, Bernard;Dawyndt, Peter
我们已经开发了essaMEM，这是一种用于寻找最大精确匹配的工具，可用于基因组比较和读段作图。essaMEM通过稀疏子数组增强了现有稀疏后缀数组实现。测试表明，用于查找最大精确匹配的增强算法要快得多，同时保持相同的内存占用。通过这种方式，稀疏后缀数组仍然可以与更复杂的压缩后缀数组竞争。可用性：源代码可以在https://github.ugent.be/ComputationalBiology/essaMEM.Contact上免费获得：Michael。Vyverman@UGent.be补充信息：补充数据可在生物信息学在线获得。
We have developed essaMEM, a tool for finding maximal exact matches that can be used in genome comparison and read mapping. essaMEM enhances an existing sparse suffix array implementation with a sparse child array. Tests indicate that the enhanced algorithm for finding maximal exact matches is much faster, while maintaining the same memory footprint. In this way, sparse suffix arrays remain competitive with the more complex compressed suffix arrays.Availability: Source code is freely available at https://github.ugent.be/ComputationalBiology/essaMEM.Contact: Michael. Vyverman@UGent.beSupplementary information: Supplementary data are available at Bioinformatics online.