DNA STRIDER - A C-PROGRAM FOR THE FAST ANALYSIS OF DNA AND PROTEIN SEQUENCES ON THE APPLE MACINTOSH FAMILY OF COMPUTERS
DNA STRIDER - A C-PROGRAM FOR THE FAST ANALYSIS OF DNA AND PROTEIN SEQUENCES ON THE APPLE MACINTOSH FAMILY OF COMPUTERS
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DOI：
10.1093/nar/16.5.1829
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发表时间：
1988-03-11
影响因子：
14.9
通讯作者：
MARCK, C
中科院分区：
文献类型：
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作者：
MARCK, C
DNA Strider是一个新的集成DNA和蛋白质序列分析程序，用C语言编写，适用于Macintosh Plus，SE和II计算机。它被设计成一个易于学习和使用的程序，以及一个快速和有效的工具，用于日常的序列分析工作。该程序由多窗口序列编辑器和各种DNA和蛋白质分析功能组成。编辑器可以使用4种不同类型的序列（DNA，简并DNA，RNA和单字母编码蛋白质），并可以同时处理6个任何类型的序列，每个序列高达32.5 kB。对于DNA序列，允许碱基的负数编号。所有经典的限制和翻译分析功能都存在，并且可以在任何开放序列或序列的一部分上以任何顺序执行。该程序的主要特点是，同一分析功能可以在不同的序列上重复多次，从而在屏幕上生成多个窗口。已经结合了许多图形功能，例如图形限制性图谱、疏水性图谱和根据Sharp和Li（1）的CAI图-密码子适应指数。酶切位点的搜索采用了一种新设计的快速六聚体前瞻算法。用130种限制性内切核酸酶的文库搜索所有位点的典型运行时间是每10000个碱基1秒。因此，pBR 322质粒的环形限制性内切酶图谱可以从其序列计算出来，并在2秒内显示在Macintosh Plus屏幕上，其多线限制性内切酶图谱可以在5秒内在滚动窗口中获得。
DNA Strider is a new integrated DNA and Protein sequence analysis program written with the C language for the Macintosh Plus, SE and II computers. It has been designed as an easy to learn and use program as well as a fast and efficient tool for the day-to-day sequence analysis work. The program consists of a multi-window sequence editor and of various DNA and Protein analysis functions. The editor may use 4 different types of sequences (DNA, degenerate DNA, RNA and one-letter coded protein) and can handle simultaneously 6 sequences of any type up to 32.5 kB each. Negative numbering of the bases is allowed for DNA sequences. All classical restriction and translation analysis functions are present and can be performed in any order on any open sequence or part of a sequence. The main feature of the program is that the same analysis function can be repeated several times on different sequences, thus generating multiple windows on the screen. Many graphic capabilities have been incorporated such as graphic restriction map, hydrophobicity profile and the CAI plot - codon adaptation index according to Sharp and Li (1). The restriction sites search uses a newly designed fast hexamer look-ahead algorithm. Typical runtime for the search of all sites with a library of 130 restriction endonucleases is 1 second per 10000 bases. The circular graphic restriction map of the pBR322 plasmid can be therefore computed from its sequence and displayed on the Macintosh Plus screen within 2 seconds and its multiline restriction map obtained in a scrolling window within 5 seconds.