Finding intron/exon splice junctions using INFO, INterruption finder and organizer
Finding intron/exon splice junctions using INFO, INterruption finder and organizer
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DOI：
10.1089/cmb.1998.5.307
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发表时间：
1998-06-01
影响因子：
1.7
通讯作者：
Smith, DW
中科院分区：
文献类型：
--
作者：
Laub, MT;Smith, DW
INFO（中断查找器和组织器）已被用于通过使用相似性矩阵和加窗算法将输入 DNA 序列的六个概念翻译与蛋白质数据库中的序列进行比较，来查找人类和其他 DNA 中的编码序列内含子-外显子剪接点。检测到的相似性既描绘了基因的位置，又提供了有关基因产物功能的线索。除了使用标准相似性矩阵和加窗算法外，INFO还使用两个新颖的步骤，即迷你库和反向序列步骤，来增强小外显子的识别并提高连接核苷酸描绘的精度，可以可靠地找到小至约30个碱基的外显子，并且当使用规范剪接连接信息时，可以精确识别> 90％的连接。通过 MiniLibrary 和 Reverse Sequence 步骤，用户无需优化 INFO 参数。在使用 19 个人类 DNA 序列进行的比较测试中，INFO 发现 111 个外显子中的 108 个外显子，报告了 0 个假阳性，而 BLASTX 有 111 个外显子和 51 个假阳性，GRAIL II 有 99 个外显子和 6 个假阳性，GeneMark 有 77 个外显子和 24 个假阳性，GeneID 有 61 个外显子和 9 个假阳性，以及 105 个外显子和 6 个假阳性对于 PROCRUSTES，查找和定位这 111 个外显子的相关系数大于 98%；对于 INFO，在 13 个非人类 DNA 序列的测试运行中获得了可比较的结果。 INFO 适用于任何物种的 DNA，随着序列数据库的扩展将变得更加强大，并补充其他启发式方法。
INFO, INterruption Finder and Organizer, has been used to find coding sequence intron-exon splice junctions in human and other DNA by comparing the six conceptual translations of the input DNA sequence with sequences in protein databanks using a similarity matrix and windowing algorithm. Similarities detected both delineate position of the gene and provide clues as to the function of the gene product. In addition to use of a standard similarity matrix and windowing algorithm, INFO uses two novel steps, the MiniLibrary and Reverse Sequence steps, to enhance identification of small exons and to improve precision of junction nucleotide delineation, Exons as small as about 30 bases can be reliably found, and >90% of junctions are precisely identified when canonical splice junction information is used. With the MiniLibrary and Reverse Sequence steps, INFO parameters need not be optimized by the user. In comparative test runs using 19 human DNA sequences, INFO found 108 of 111 exons, with 0 reported false positives, compared with 111 exons and 51 false positives for BLASTX, 99 exons and 6 false positives for GRAIL II, 77 exons and 24 false positives for GeneMark, 61 exons and 9 false positives for GeneID, and 105 exons and 6 false positives for PROCRUSTES, The correlation coefficient for finding and positioning these 111 exons was greater than 98% for INFO, Comparable results were obtained in test runs of 13 nonhuman DNA sequences. INFO is applicable to DNA from any species, will become more robust as sequence databanks expand, and complements other heuristic approaches.