Institute of Parasitology, McGill University, 21,111 Lakeshore Road, Ste. Anne de Bellevue, Montreal, Quebec H9X3V9, Canada.
Trends Parasitol. 2010 May;26(5):225-9. doi: 10.1016/j.pt.2010.02.001. Epub 2010 Mar 6.
The genomes of trypanosomatids are distantly related to other eukaryotes, with significant numbers of hypothetical or conserved hypothetical trypanosomatid-specific genes, whose functions cannot be determined using homology-dependent annotation methods. Here, we describe homology-independent methods to infer biological functions of genes based solely on their sequences. These approaches are not limited to trypanosomatid genomes and provide grounds for analysis of genomes of Plasmodium falciparum and other parasites associated with neglected tropical diseases. A critical evaluation of the current state of annotation of parasitic genomes endorses the need to exploit homology-independent computational methods, which can identify protein functions, potentially including essential genes, and provide a plethora of valuable information on interaction networks and regulatory elements.
动基体生物的基因组与其他真核生物的基因组关系较远，存在大量假定的或保守的动基体生物特有的假定基因，这些基因的功能无法使用基于同源性的注释方法来确定。在这里，我们描述了仅基于基因序列推断基因生物学功能的与同源性无关的方法。这些方法不仅限于动基体生物基因组，为分析疟原虫和其他与被忽视的热带病相关的寄生虫的基因组提供了依据。对寄生虫基因组注释现状的批判性评估证实了有必要利用与同源性无关的计算方法，这些方法可以识别蛋白质功能，可能包括必需基因，并提供大量关于相互作用网络和调控元件的有价值的信息。
