KinFin: Software for Taxon-Aware Analysis of Clustered Protein Sequences.
KinFin: Software for Taxon-Aware Analysis of Clustered Protein Sequences.
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DOI：
10.1534/g3.117.300233
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发表时间：
2017-10-05
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影响因子：
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通讯作者：
Blaxter ML
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作者：
Laetsch DR;Blaxter ML
比较基因组学研究的是生物体基因组中编码的信息之间的相似性和差异性。一种常见的方法是通过基于序列相似性聚类蛋白质序列来定义基因家族，并分析不同物种组中蛋白质簇的存在和不存在，作为生物学的指导。由于这些数据的高维性，从大量物种或具有许多基因的物种推断的蛋白质簇的下游分析是不平凡的，并且存在用于透明、可再现和可定制分析的解决方案。我们推出了KinFin，这是一种简化的软件解决方案，能够集成常见文件格式的数据并提供蛋白质簇的聚合注释。KinFin基于所分析物种的系统分类学或用户定义的分类群进行分析，例如，基于生活史特征，生物表型或竞争性系统发育假设等属性的集合。结果通过图形和详细的文本输出文件报告。我们通过解决有关丝虫线虫生物学的问题来说明KinFin管道的实用性，其中包括具有兽医和医学重要性的寄生虫。我们解决了物种之间的系统发育关系，并探索关键谱系和自定义分类单元集之间的蛋白质簇的功能注释，确定感兴趣的基因家族。KinFin可以很容易地集成到现有的比较基因组工作流程中，并促进聚类蛋白质数据的透明和可重复分析。
The field of comparative genomics is concerned with the study of similarities and differences between the information encoded in the genomes of organisms. A common approach is to define gene families by clustering protein sequences based on sequence similarity, and analyze protein cluster presence and absence in different species groups as a guide to biology. Due to the high dimensionality of these data, downstream analysis of protein clusters inferred from large numbers of species, or species with many genes, is nontrivial, and few solutions exist for transparent, reproducible, and customizable analyses. We present KinFin, a streamlined software solution capable of integrating data from common file formats and delivering aggregative annotation of protein clusters. KinFin delivers analyses based on systematic taxonomy of the species analyzed, or on user-defined, groupings of taxa, for example, sets based on attributes such as life history traits, organismal phenotypes, or competing phylogenetic hypotheses. Results are reported through graphical and detailed text output files. We illustrate the utility of the KinFin pipeline by addressing questions regarding the biology of filarial nematodes, which include parasites of veterinary and medical importance. We resolve the phylogenetic relationships between the species and explore functional annotation of proteins in clusters in key lineages and between custom taxon sets, identifying gene families of interest. KinFin can easily be integrated into existing comparative genomic workflows, and promotes transparent and reproducible analysis of clustered protein data.