用于定位两个序列之间相似性的对角线遍历同源性搜索算法。
The diagonal-traverse homology search algorithm for locating similarities between two sequences.
作者信息
White C T, Hardies S C, Hutchison C A, Edgell M H
出版信息
Nucleic Acids Res. 1984 Jan 11;12(1 Pt 2):751-66. doi: 10.1093/nar/12.1part2.751.
Abstract
We present a fast computer algorithm for finding homology between two DNA sequences. It generates a two-dimensional display in which a diagonal string of dots represents a stretch of homology between the two sequences. Our algorithm performs the search very rapidly, and has no internal data storage requirement except for the sequences themselves. These characteristics make it particularly well suited for execution on microcomputers. Without slowing execution, the matching criterion can be that a specified fraction of contiguous bases must be identical. Even with gapped sequences, we have found large search windows to be surprisingly good for detecting poor homologies with nearly complete background suppression. A diagonal search pattern is used that reports the finds in a compact and logically ordered form. A simple and rapid plotting algorithm for unsophisticated printers is also reported.
摘要
我们提出了一种用于寻找两个DNA序列之间同源性的快速计算机算法。它生成一个二维显示，其中对角线上的一串点表示两个序列之间的一段同源性。我们的算法执行搜索速度非常快，除了序列本身外没有内部数据存储要求。这些特性使其特别适合在微型计算机上执行。在不降低执行速度的情况下，匹配标准可以是指定比例的相邻碱基必须相同。即使对于有缺口的序列，我们发现大的搜索窗口对于检测同源性较差且几乎完全抑制背景的情况也出奇地有效。使用对角搜索模式以紧凑且逻辑有序的形式报告发现结果。还报告了一种适用于简单打印机的简单快速绘图算法。
相似文献
1
The diagonal-traverse homology search algorithm for locating similarities between two sequences.用于定位两个序列之间相似性的对角线遍历同源性搜索算法。
Nucleic Acids Res. 1984 Jan 11;12(1 Pt 2):751-66. doi: 10.1093/nar/12.1part2.751.
2
A high speed, high capacity homology matrix: zooming through SV40 and polyoma.一种高速、高容量的同源性矩阵：快速分析猿猴病毒40和多瘤病毒
Nucleic Acids Res. 1982 Aug 11;10(15):4765-82. doi: 10.1093/nar/10.15.4765.
3
Similarities in the structural organization of the genomes of stumptailed macaque virus (strain HD) and simian virus 40.断尾猕猴病毒（HD株）与猴病毒40基因组结构组织的相似性。
J Gen Virol. 1979 Oct;45(1):223-6. doi: 10.1099/0022-1317-45-1-223.
4
Should nucleotide sequence analyzing computer algorithms always extend homologies by extending homologies?核苷酸序列分析计算机算法是否总是通过延伸同源性来扩展同源性？
Nucleic Acids Res. 1986 Jan 10;14(1):425-30. doi: 10.1093/nar/14.1.425.
5
Interactive computer programs for the graphic analysis of nucleotide sequence data.用于核苷酸序列数据图形分析的交互式计算机程序。
Nucleic Acids Res. 1984 Jan 11;12(1 Pt 2):665-73. doi: 10.1093/nar/12.1part2.665.
6
Color graphics representations of large sequences in the GEM environment.GEM环境中大型序列的彩色图形表示。
Nucleic Acids Res. 1988 Mar 11;16(5):1657-66. doi: 10.1093/nar/16.5.1657.
7
'DNA Strider': a 'C' program for the fast analysis of DNA and protein sequences on the Apple Macintosh family of computers.“DNA Strider”：一款用于在苹果麦金塔系列计算机上快速分析DNA和蛋白质序列的“C”程序。
Nucleic Acids Res. 1988 Mar 11;16(5):1829-36. doi: 10.1093/nar/16.5.1829.
8
Two-dimensional graphic analysis of DNA sequence homologies.DNA序列同源性的二维图形分析
Nucleic Acids Res. 1982 Jan 11;10(1):365-74. doi: 10.1093/nar/10.1.365.
9
A comprehensive sequence analysis program for the IBM personal computer.一款适用于IBM个人计算机的综合序列分析程序。
Nucleic Acids Res. 1984 Jan 11;12(1 Pt 2):581-99. doi: 10.1093/nar/12.1part2.581.
10
An interactive dot matrix system for locating potentially significant features in nucleic acid molecules.
J Biomol Struct Dyn. 1987 Apr;4(5):697-706. doi: 10.1080/07391102.1987.10507673.
引用本文的文献
1
A retroviral provirus closely associated with the Ren-2 gene of DBA/2 mice.一种与DBA/2小鼠的Ren-2基因密切相关的逆转录病毒前病毒。
Nucleic Acids Res. 1984 Nov 26;12(22):8579-93. doi: 10.1093/nar/12.22.8579.
2
Analysis of the complete nucleotide sequence of the group IV RNA coliphage SP.IV 组 RNA 大肠杆菌噬菌体 SP 的全核苷酸序列分析。
Nucleic Acids Res. 1988 Jul 11;16(13):6205-21. doi: 10.1093/nar/16.13.6205.
3
The F-type 5' motif of mouse L1 elements: a major class of L1 termini similar to the A-type in organization but unrelated in sequence.小鼠L1元件的F型5'基序：一类主要的L1末端，其结构与A型相似，但序列无关。
Nucleic Acids Res. 1988 Jan 25;16(2):739-49. doi: 10.1093/nar/16.2.739.
4
Nucleotide sequence of the delta-beta-globin intergenic segment in the macaque: structure and evolutionary rates in higher primates.猕猴δ-珠蛋白基因间隔区的核苷酸序列：高等灵长类动物的结构与进化速率
J Mol Evol. 1987;24(4):297-308. doi: 10.1007/BF02134128.
5
Effects of heavy metals on Drosophila larvae and a metallothionein cDNA.重金属对果蝇幼虫及一种金属硫蛋白cDNA的影响。
Environ Health Perspect. 1986 Mar;65:107-16. doi: 10.1289/ehp.8665107.
6
Structure of the Saccharomyces cerevisiae HO gene and analysis of its upstream regulatory region.酿酒酵母HO基因的结构及其上游调控区域分析
Mol Cell Biol. 1986 Dec;6(12):4281-94. doi: 10.1128/mcb.6.12.4281-4294.1986.
7
Fast analysis of DNA and protein sequence on Apple IIe: restriction sites search, alignment of short sequence and dot matrix analysis.在苹果IIe计算机上对DNA和蛋白质序列进行快速分析：限制酶切位点搜索、短序列比对及点阵分析。
Nucleic Acids Res. 1986 Jan 10;14(1):583-90. doi: 10.1093/nar/14.1.583.
8
Activation regions in a yeast transposon have homology to mating type control sequences and to mammalian enhancers.酵母转座子中的激活区域与交配型控制序列以及哺乳动物增强子具有同源性。
Proc Natl Acad Sci U S A. 1985 Aug;82(16):5423-7. doi: 10.1073/pnas.82.16.5423.
本文引用的文献
1
Optimal sequence alignments.最佳序列比对。
Proc Natl Acad Sci U S A. 1983 Mar;80(5):1382-6. doi: 10.1073/pnas.80.5.1382.
2
Complete nucleotide sequence of the human delta-globin gene.人类δ-珠蛋白基因的完整核苷酸序列。
Cell. 1980 Oct;21(3):639-46. doi: 10.1016/0092-8674(80)90427-4.
3
An interactive graphics program for comparing and aligning nucleic acid and amino acid sequences.一个用于比较和比对核酸及氨基酸序列的交互式图形程序。
Nucleic Acids Res. 1982 May 11;10(9):2951-61. doi: 10.1093/nar/10.9.2951.
4
Two-dimensional graphic analysis of DNA sequence homologies.DNA序列同源性的二维图形分析
Nucleic Acids Res. 1982 Jan 11;10(1):365-74. doi: 10.1093/nar/10.1.365.
5
The DNA sequence of the 5' flanking region of the human beta-globin gene: evolutionary conservation and polymorphic differences.人类β-珠蛋白基因5'侧翼区的DNA序列：进化保守性与多态性差异
Nucleic Acids Res. 1982 Mar 25;10(6):2109-20. doi: 10.1093/nar/10.6.2109.
6
Enhanced graphic matrix analysis of nucleic acid and protein sequences.核酸和蛋白质序列的增强图形矩阵分析
Proc Natl Acad Sci U S A. 1981 Dec;78(12):7665-9. doi: 10.1073/pnas.78.12.7665.
7
Matrix program to analyze primary structure homology.用于分析一级结构同源性的矩阵程序。
Nucleic Acids Res. 1982 Jan 11;10(1):127-31. doi: 10.1093/nar/10.1.127.
8
Three cDNA clones encoding mouse transplantation antigens: homology to immunoglobulin genes.三个编码小鼠移植抗原的cDNA克隆：与免疫球蛋白基因的同源性
Cell. 1981 Apr;24(1):125-34. doi: 10.1016/0092-8674(81)90508-0.
9
A high speed, high capacity homology matrix: zooming through SV40 and polyoma.一种高速、高容量的同源性矩阵：快速分析猿猴病毒40和多瘤病毒
Nucleic Acids Res. 1982 Aug 11;10(15):4765-82. doi: 10.1093/nar/10.15.4765.
10
Interactive computer programs in sequence data analysis.序列数据分析中的交互式计算机程序。
Nucleic Acids Res. 1982 Jan 11;10(1):433-47. doi: 10.1093/nar/10.1.433.
Zotero 插件