nail: software for high-speed, high-sensitivity protein sequence annotation.
nail: software for high-speed, high-sensitivity protein sequence annotation.
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nail：用于高速、高灵敏度蛋白质序列注释的软件。
DOI：
10.1101/2024.01.27.577580
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发表时间：
2024
期刊：
影响因子：
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通讯作者：
Wheeler,TravisJ
中科院分区：
文献类型：
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作者：
Roddy,JackW;Rich,DavidH;Wheeler,TravisJ
“快固然好，但准确才是最重要的。”背景：新测序生物的极端多样性和现代序列数据库的相当大的规模导致了序列注释的敏感性和速度的竞争需求之间的紧张关系，多个工具在一个轴或另一个轴上取代了古老的BLAST软件套件。基于剖面隐马尔可夫模型（phmm）的比对已经证明了最先进的灵敏度，而最近的算法进步已经导致了超快速的注释工具，其灵敏度接近BLAST。结果：在这里，我们介绍了一个新的工具，它弥合了这两个方向的进步之间的差距，达到了与快速注释方法（如MMseqs2）相当的速度，同时保留了phmm提供的大部分灵敏度。该工具名为nail，通过识别FB动态规划矩阵中包含大部分概率质量的单元的稀疏子集，实现了pHMM前向/后向（FB）算法的启发式近似。该方法产生了pHMM分数和e值的精确近似值，具有高速度和小内存需求。在蛋白质基准测试中，nail恢复了MMseqs2和HMMER之间的大部分召回差异，运行时间比HMMER3快约26倍（仅比MMseqs2的敏感变体慢约2.4倍）。nail在开放的BSD-3-clause许可下发布，可从https://github.com/TravisWheelerLab/nail下载。
“ Fast is fine, but accuracy is final. ” -- Wyatt Earp Background: The extreme diversity of newly sequenced organisms and considerable scale of modern sequence databases lead to a tension between competing needs for sensitivity and speed in sequence annotation, with multiple tools displacing the venerable BLAST software suite on one axis or another. Alignment based on profile hidden Markov models (pHMMs) has demonstrated state of art sensitivity, while recent algorithmic advances have resulted in hyper-fast annotation tools with sensitivity close to that of BLAST. Results: Here, we introduce a new tool that bridges the gap between advances in these two directions, reaching speeds comparable to fast annotation methods such as MMseqs2 while retaining most of the sensitivity offered by pHMMs. The tool, called nail, implements a heuristic approximation of the pHMM Forward/Backward (FB) algorithm by identifying a sparse subset of the cells in the FB dynamic programming matrix that contains most of the probability mass. The method produces an accurate approximation of pHMM scores and E-values with high speed and small memory requirements. On a protein benchmark, nail recovers the majority of recall difference between MMseqs2 and HMMER, with run time ~26x faster than HMMER3 (only ~2.4x slower than MMseqs2’s sensitive variant). nail is released under the open BSD-3-clause license and is available for download at https://github.com/TravisWheelerLab/nail.