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软件简介： <trans data-src="libgapmis: extending short-read alignments. ">libgapmis：扩展短读对齐。</trans><trans data-src="BACKGROUND: A wide variety of short-read alignment programmes have been published recently to tackle the problem of mapping millions of short reads to a reference genome, focusing on different aspects of the procedure such as time and memory efficiency, sensitivity, and accuracy. ">背景：最近出版了各种各样的短读比对程序，以解决将数百万个短阅读映射到参考基因组的问题，重点关注程序的不同方面，如时间和记忆效率、灵敏度和准确性。</trans><trans data-src="These tools allow for a small number of mismatches in the alignment; ">这些工具允许对齐中出现少量不匹配；</trans><trans data-src="however, their ability to allow for gaps varies greatly, with many performing poorly or not allowing them at all. ">然而，他们允许差距的能力差异很大，许多人表现不佳或根本不允许。</trans><trans data-src="The seed-and-extend strategy is applied in most short-read alignment programmes. ">种子和扩展策略应用于大多数短读对齐程序。</trans><trans data-src="After aligning a substring of the reference sequence against the high-quality prefix of a short read--the seed--an important problem is to find the best possible alignment between a substring of the reference sequence succeeding and the remaining suffix of low quality of the read--extend. ">在将参考序列的子串与短读的高质量前缀（seed）对齐之后，一个重要的问题是在后续的参考序列的子串和剩余的低质量读取后缀之间找到可能的最佳对齐方式。</trans><trans data-src="The fact that the reads are rather short and that the gap occurrence frequency observed in various studies is rather low suggest that aligning (parts of) those reads with a single gap is in fact desirable. ">事实上，阅读时间很短，而且在各种研究中观察到的空白出现频率相当低，这表明将这些阅读（部分）与单个空白对齐实际上是可取的。</trans><trans data-src="RESULTS: In this article, we present libgapmis, a library for extending pairwise short-read alignments. ">结果：在本文中，我们介绍了libgapmis，一个扩展成对短读对齐的库。</trans><trans data-src="Apart from the standard CPU version, it includes ultrafast SSE- and GPU-based implementations. ">除了标准的CPU版本，它还包括基于SSE和GPU的超快实现。</trans><trans data-src="libgapmis is based on an algorithm computing a modified version of the traditional dynamic-programming matrix for sequence alignment. ">libgapmis基于一种算法，它是对传统动态规划矩阵进行序列比对的一种改进版本。</trans><trans data-src="Extensive experimental results demonstrate that the functions of the CPU version provided in this library accelerate the computations by a factor of 20 compared to other programmes. ">大量的实验结果表明，与其他程序相比，这个库中提供的CPU版本的功能使计算速度提高了20倍。</trans><trans data-src="The analogous SSE- and GPU-based implementations accelerate the computations by a factor of 6 and 11, respectively, compared to the CPU version. ">与CPU版本相比，类似的基于SSE和GPU的实现将计算速度分别提高了6倍和11倍。</trans><trans data-src="The library also provides the user the flexibility to split the read into fragments, based on the observed gap occurrence frequency and the length of the read, thereby allowing for a variable, but bounded, number of gaps in the alignment. ">该库还为用户提供了根据观察到的间隙发生频率和读取长度将读取拆分为片段的灵活性，从而允许对齐中存在可变但有限制的间隙数量。</trans><trans data-src="CONCLUSIONS: We present libgapmis, a library for extending pairwise short-read alignments. ">结论：我们提出了libgapmis，一个扩展成对短阅读比对的库。</trans><trans data-src="We show that libgapmis is better-suited and more efficient than existing algorithms for this task. ">我们证明libgapmis比现有的算法更适合这个任务，并且效率更高。</trans><trans data-src="The importance of our contribution is underlined by the fact that the provided functions may be seamlessly integrated into any short-read alignment pipeline. ">所提供的功能可以无缝地集成到任何短读对齐管道中，这一事实突显了我们贡献的重要性。</trans><trans data-src="The open-source code of libgapmis is available at ">libgapmis的开源代码可以在</trans><trans data-src="http://www.exelixis-lab.org/gapmis.">http://www.exelixis-lab.org/gapmis。</trans>

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（例如，对于GAP：“GAP 4型系统组织代数算法”，Zbl 0918.68050）

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评论： <trans data-src="Update software libgapmis: ">更新软件libgapmis：</trans><trans data-src="http://swmath.org/software/24065">http://swmath.org/software/24065</trans>

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