Background

Reconstruction of amino acid sequences from assembled transcriptome is of interest in personalized medicine, for example, to predict drug-target (or protein-protein) interaction considering individual’s genomic variations. Most of the existing transcriptome assemblers, however, seems not well suited for this purpose.

Methods

In this work, we present StringFix, an annotation guided transcriptome assembly and protein sequence reconstruction software tool that takes genome-aligned reads and the annotations associated to the reference genome as input. The tool ‘fixes’ the pre-annotated transcript sequence by taking small variations into account, finally to produce possible amino acid sequences that are likely to exist in the test tissue.

Results

The results show that, using outputs from existing reference-based assemblers as the input GTF-guide, StringFix could reconstruct amino acid sequences more precisely with higher sensitivity than direct generation using the recovered transcripts from all the assemblers we tested.

Conclusion

By using StringFix with the existing reference-based assemblers, one can recover not only a novel transcripts and isoforms but also the possible amino acid sequence stemming from them.

中文翻译：

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StringFix：注释引导的转录组组装器提高了 RNA-Seq 读取中氨基酸序列的恢复

背景

从组装的转录组中重建氨基酸序列在个性化医疗中很有意义，例如，考虑个体的基因组变异来预测药物-靶标（或蛋白质-蛋白质）相互作用。然而，大多数现有的转录组组装程序似乎不太适合此目的。

方法

在这项工作中，我们提出了 StringFix，一种注释引导的转录组组装和蛋白质序列重建软件工具，它将基因组对齐的读数和与参考基因组相关的注释作为输入。该工具通过考虑微小的变化来“修复”预先注释的转录序列，最终产生测试组织中可能存在的可能的氨基酸序列。

结果

结果表明，与使用我们测试的所有组装器恢复的转录本直接生成相比，使用现有基于参考的组装器的输出作为输入 GTF 指南，StringFix 可以更精确地重建氨基酸序列，并且灵敏度更高。

结论

通过将 StringFix 与现有的基于参考的组装程序结合使用，人们不仅可以恢复新的转录本和亚型，还可以恢复源自它们的可能的氨基酸序列。