Degroeve Sven, Saeys Yvan, De Baets Bernard, Rouzé Pierre, Van de Peer Yves
Department of Plant Systems Biology, Flanders Interuniversity Institute for Biotechnology (VIB), Technologiepark 927, Gent 9052, Belgium.
Bioinformatics. 2005 Apr 15;21(8):1332-8. doi: 10.1093/bioinformatics/bti166. Epub 2004 Nov 25.
In this age of complete genome sequencing, finding the location and structure of genes is crucial for further molecular research. The accurate prediction of intron boundaries largely facilitates the correct prediction of gene structure in nuclear genomes. Many tools for localizing these boundaries on DNA sequences have been developed and are available to researchers through the internet. Nevertheless, these tools still make many false positive predictions.
This manuscript presents a novel publicly available splice site prediction tool named SpliceMachine that (i) shows state-of-the-art prediction performance on Arabidopsis thaliana and human sequences, (ii) performs a computationally fast annotation and (iii) can be trained by the user on its own data.
Results, figures and software are available at http://www.bioinformatics.psb.ugent.be/supplementary_data/
在全基因组测序的这个时代，确定基因的位置和结构对于进一步的分子研究至关重要。准确预测内含子边界在很大程度上有助于正确预测核基因组中的基因结构。已经开发了许多用于在DNA序列上定位这些边界的工具，研究人员可以通过互联网获取这些工具。然而，这些工具仍然会做出许多假阳性预测。
本手稿介绍了一种名为SpliceMachine的新型公开可用剪接位点预测工具，该工具（i）在拟南芥和人类序列上展示了最先进的预测性能，（ii）执行计算速度快的注释，并且（iii）用户可以根据自己的数据对其进行训练。
结果、图表和软件可在http://www.bioinformatics.psb.ugent.be/supplementary_data/获取。
