Sensitive and error-tolerant annotation of protein-coding DNA with BATH.

IF 2.4 Q2 MATHEMATICAL & COMPUTATIONAL BIOLOGY
Bioinformatics advances Pub Date : 2024-06-14 eCollection Date: 2024-01-01 DOI:10.1093/bioadv/vbae088
Genevieve R Krause, Walt Shands, Travis J Wheeler
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引用次数: 0

Abstract

Summary: We present BATH, a tool for highly sensitive annotation of protein-coding DNA based on direct alignment of that DNA to a database of protein sequences or profile hidden Markov models (pHMMs). BATH is built on top of the HMMER3 code base, and simplifies the annotation workflow for pHMM-based translated sequence annotation by providing a straightforward input interface and easy-to-interpret output. BATH also introduces novel frameshift-aware algorithms to detect frameshift-inducing nucleotide insertions and deletions (indels). BATH matches the accuracy of HMMER3 for annotation of sequences containing no errors, and produces superior accuracy to all tested tools for annotation of sequences containing nucleotide indels. These results suggest that BATH should be used when high annotation sensitivity is required, particularly when frameshift errors are expected to interrupt protein-coding regions, as is true with long-read sequencing data and in the context of pseudogenes.

Availability and implementation: The software is available at https://github.com/TravisWheelerLab/BATH.

利用 BATH 对蛋白质编码 DNA 进行灵敏且容错的注释。
摘要:我们介绍的 BATH 是一种对蛋白质编码 DNA 进行高灵敏度注释的工具,它基于 DNA 与蛋白质序列数据库或轮廓隐马尔可夫模型(pHMM)的直接比对。BATH 建立在 HMMER3 代码基础之上,通过提供简单明了的输入界面和易于理解的输出结果,简化了基于 pHMM 的翻译序列注释工作流程。BATH 还引入了新颖的帧移感知算法,以检测帧移诱导的核苷酸插入和缺失(indels)。在注释不含错误的序列时,BATH 的准确性与 HMMER3 相当,而在注释含核苷酸嵌合的序列时,其准确性优于所有测试工具。这些结果表明,当需要高注释灵敏度时,尤其是当换帧错误可能会打断蛋白质编码区时,应使用 BATH,长读数测序数据和假基因的情况就是如此:该软件可在 https://github.com/TravisWheelerLab/BATH 上获取。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
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CiteScore
1.60
自引率
0.00%
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