Sim4cc: a cross-species spliced alignment program.
Sim4cc: a cross-species spliced alignment program.
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DOI：
10.1093/nar/gkp319
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发表时间：
2009-06
影响因子：
14.9
通讯作者：
Florea L
中科院分区：
文献类型：
--
作者：
Zhou L;Pertea M;Delcher AL;Florea L
测序技术的进步加速了新基因组的测序，远远超过了注释它们所需的基因和蛋白质资源的产生。直接比较和比对来自相关物种的现有cDNA序列是确定新基因组中基因的有效且容易获得的手段。目前的剪接比对程序不足以比较不同物种之间的序列，由于其低灵敏度和剪接点的准确性。一个新的拼接比对工具，sim4cc，克服了早期的工具中的问题，结合了三个新的功能：通用间隔种子，以提高灵敏度，并允许在不同的进化距离物种之间的比较，强大的剪接信号模型和进化意识的比对技术，以提高基因模型的准确性。当在不同进化距离的脊椎动物比较中进行测试时，与现有的比对程序相比，sim4cc具有显着更高的灵敏度，在某些比较中比最接近的竞争对手高出10%以上，同时在速度上与其前身sim4相当。Sim4cc可用于基因组和cDNA序列的一对一或一对多比较，也可有效地纳入高通量注释引擎，如通过将64 000个水青冈454 EST和unigenes映射到白杨基因组所证明的。
Advances in sequencing technologies have accelerated the sequencing of new genomes, far outpacing the generation of gene and protein resources needed to annotate them. Direct comparison and alignment of existing cDNA sequences from a related species is an effective and readily available means to determine genes in the new genomes. Current spliced alignment programs are inadequate for comparing sequences between different species, owing to their low sensitivity and splice junction accuracy. A new spliced alignment tool, sim4cc, overcomes problems in the earlier tools by incorporating three new features: universal spaced seeds, to increase sensitivity and allow comparisons between species at various evolutionary distances, and powerful splice signal models and evolutionarily-aware alignment techniques, to improve the accuracy of gene models. When tested on vertebrate comparisons at diverse evolutionary distances, sim4cc had significantly higher sensitivity compared to existing alignment programs, more than 10% higher than the closest competitor for some comparisons, while being comparable in speed to its predecessor, sim4. Sim4cc can be used in one-to-one or one-to-many comparisons of genomic and cDNA sequences, and can also be effectively incorporated into a high-throughput annotation engine, as demonstrated by the mapping of 64 000 Fagus grandifolia 454 ESTs and unigenes to the poplar genome.
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