GMAP: a genomic mapping and alignment program for mRNA and EST sequences
GMAP: a genomic mapping and alignment program for mRNA and EST sequences
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DOI：
10.1093/bioinformatics/bti310
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发表时间：
2005-05-01
期刊：
影响因子：
5.8
通讯作者：
Watanabe, CK
中科院分区：
文献类型：
--
作者：
Wu, TD;Watanabe, CK
动机：我们介绍了gmap，一个独立的程序，用于映射和比对cDNA序列的基因组。该程序以最小的启动时间和内存需求映射和对齐单个序列，并提供大型序列集的快速批处理。该程序生成准确的基因结构，即使在大量的多态性和序列错误的存在下，而不使用概率剪接位点模型。该计划的基本方法包括用于基因组作图的最小采样策略、用于近似比对的寡聚体链、用于剪接位点检测的夹心DP以及具有统计学显著性检验的微外显子鉴定。在一组随机突变率为1%和3%的人类信使RNA上，gmap在超过99.3%的序列中准确地识别了所有剪接位点，这是现有程序错误率的十分之一。在大量人类表达序列标签上，gmap比blat提供更高质量的比对。在一组拟南芥cDNA上，gmap用GeneSeqer进行测序。在这些实验中，gmap的速度比现有程序提高了几倍。
Motivation: We introduce gmap, a standalone program for mapping and aligning cDNA sequences to a genome. The program maps and aligns a single sequence with minimal startup time and memory requirements, and provides fast batch processing of large sequence sets. The program generates accurate gene structures, even in the presence of substantial polymorphisms and sequence errors, without using probabilistic splice site models. Methodology underlying the program includes a minimal sampling strategy for genomic mapping, oligomer chaining for approximate alignment, sandwich DP for splice site detection, and microexon identification with statistical significance testing.Results: On a set of human messenger RNAs with random mutations at a 1 and 3% rate, gmap identified all splice sites accurately in over 99.3% of the sequences, which was one-tenth the error rate of existing programs. On a large set of human expressed sequence tags, gmap provided higher-quality alignments more often than blat did. On a set of Arabidopsis cDNAs, gmap performed comparably with GeneSeqer. In these experiments, gmap demonstrated a several-fold increase in speed over existing programs.