Mirage2's high-quality spliced protein-to-genome mappings produce accurate multiple-sequence alignments of isoforms.
Mirage2's high-quality spliced protein-to-genome mappings produce accurate multiple-sequence alignments of isoforms.
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DOI：
10.1371/journal.pone.0285225
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发表时间：
2023
期刊：
影响因子：
3.7
通讯作者：
Wheeler, Travis
中科院分区：
文献类型：
--
作者：
Nord, Alexander;Wheeler, Travis
将同源蛋白质序列组织成多序列比对（MSA）是现代蛋白质分析的基石。最近的重点是在疾病和细胞生物学中的选择性剪接异构体的重要性，突出了MSA软件的需要，可以适当地考虑异构体和外显子长度插入或缺失，异构体可能有相对于彼此。我们以前开发的幻影，软件包生成跨多个物种的异构体的MSA。在这里，我们介绍Miracle 2，它保留了原始Mirage实现的基本算法，同时提供了大幅改进的翻译映射，并提高了可用性的几个方面。我们证明，Mirobi2是非常有效的映射蛋白质，其编码外显子，这些蛋白质基因组映射导致非常准确的内含子感知对齐。此外，Mirocket 2实现了许多工程改进，简化了安装和使用。
The organization of homologous protein sequences into multiple sequence alignments (MSAs) is a cornerstone of modern analysis of proteins. Recent focus on the importance of alternatively-spliced isoforms in disease and cell biology has highlighted the need for MSA software that can appropriately account for isoforms and the exon-length insertions or deletions that isoforms may have relative to each other. We previously developed Mirage, a software package for generating MSAs for isoforms spanning multiple species. Here, we present Mirage2, which retains the fundamental algorithms of the original Mirage implementation while providing substantially improved translated mapping and improving several aspects of usability. We demonstrate that Mirage2 is highly effective at mapping proteins to their encoding exons, and that these protein-genome mappings lead to extremely accurate intron-aware alignments. Additionally, Mirage2 implements a number of engineering improvements that simplify installation and use.
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DOI：
10.1073/pnas.89.22.10915
发表时间：
1992-11-15
影响因子：
11.1
作者：
HENIKOFF, S;HENIKOFF, JG
通讯作者：
HENIKOFF, JG
影响因子：
4.6
作者：
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影响因子：
10.7
作者：
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通讯作者：
Standley DM
影响因子：
14.9
作者：
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