Department of Molecular Biology and Genetics, Democritus University of Thrace, University Campus, 68100 Alexandroupolis, Greece.
Comput Methods Programs Biomed. 2013 Sep;111(3):711-4. doi: 10.1016/j.cmpb.2013.05.021. Epub 2013 Jun 22.
We present Pinda, a Web service for the detection and analysis of possible duplications of a given protein or DNA sequence within a source species. Pinda fully automates the whole gene duplication detection procedure, from performing the initial similarity searches, to generating the multiple sequence alignments and the corresponding phylogenetic trees, to bootstrapping the trees and producing a Z-score-based list of duplication candidates for the input sequence. Pinda has been cross-validated using an extensive set of known and bibliographically characterized duplication events. The service facilitates the automatic and dependable identification of gene duplication events, using some of the most successful bioinformatics software to perform an extensive analysis protocol. Pinda will prove of use for the analysis of newly discovered genes and proteins, thus also assisting the study of recently sequenced genomes. The service's location is http://orion.mbg.duth.gr/Pinda. The source code is freely available via https://github.com/dgkontopoulos/Pinda/.
我们介绍 Pinda，这是一个用于在给定物种的蛋白质或 DNA 序列中检测和分析可能的重复的 Web 服务。Pinda 完全自动化了整个基因重复检测过程，从执行初始相似性搜索，到生成多序列比对和相应的系统发育树，再到对输入序列进行自举和生成基于 Z 分数的重复候选列表。Pinda 已经使用广泛的已知和文献特征化的重复事件进行了交叉验证。该服务使用一些最成功的生物信息学软件来执行广泛的分析协议，方便了基因重复事件的自动和可靠识别。Pinda 将有助于分析新发现的基因和蛋白质，从而也有助于最近测序的基因组的研究。该服务的位置是 http://orion.mbg.duth.gr/Pinda。源代码可通过 https://github.com/dgkontopoulos/Pinda/ 免费获取。
