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我们序列处理软件的当前状态与便携性。

The current status and portability of our sequence handling software.

作者信息

Staden R

出版信息

Nucleic Acids Res. 1986 Jan 10;14(1):217-31. doi: 10.1093/nar/14.1.217.

DOI:10.1093/nar/14.1.217
PMID:3511446
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC339382/
Abstract

I describe the current status of our sequence analysis software. The package contains a comprehensive suite of programs for managing large shotgun sequencing projects, a program containing 61 functions for analysing single sequences and a program for comparing pairs of sequences for similarity. The programs that have been described before have been improved by the addition of new functions and by being made very much easier to use. The major interactive programs have 125 pages of online help available from within them. Several new programs are described including screen editing of aligned gel readings for shotgun sequencing projects; a method to highlight errors in aligned gel readings, new methods for searching for putative signals in sequences. We use the programs on a VAX computer but the whole package has been rewritten to make it easy to transport it to other machines. I believe the programs will now run on any machine with a FORTRAN77 compiler and sufficient memory. We are currently putting the programs onto an IBM PC XT/AT and another micro running under UNIX.

摘要

我描述了我们序列分析软件的当前状态。该软件包包含一套用于管理大型鸟枪法测序项目的综合程序、一个包含61个用于分析单序列功能的程序以及一个用于比较成对序列相似性的程序。之前描述过的程序通过添加新功能和使其更易于使用得到了改进。主要的交互式程序中有125页的在线帮助。描述了几个新程序，包括用于鸟枪法测序项目的比对凝胶读数的屏幕编辑；一种突出显示比对凝胶读数中错误的方法、在序列中搜索假定信号的新方法。我们在VAX计算机上使用这些程序，但整个软件包已被重写以便于移植到其他机器上。我相信这些程序现在可以在任何具有FORTRAN77编译器和足够内存的机器上运行。我们目前正在将这些程序安装到IBM PC XT/AT和另一台运行UNIX的微型计算机上。

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本文引用的文献

1
Automation of the computer handling of gel reading data produced by the shotgun method of DNA sequencing.DNA测序鸟枪法产生的凝胶读数数据的计算机处理自动化。
Nucleic Acids Res. 1982 Aug 11;10(15):4731-51. doi: 10.1093/nar/10.15.4731.
2
Use of the 'Perceptron' algorithm to distinguish translational initiation sites in E. coli.使用“感知器”算法区分大肠杆菌中的翻译起始位点。
Nucleic Acids Res. 1982 May 11;10(9):2997-3011. doi: 10.1093/nar/10.9.2997.
3
Structure and variation of human alpha 1-antitrypsin.人类α1-抗胰蛋白酶的结构与变异
Nature. 1982 Jul 22;298(5872):329-34. doi: 10.1038/298329a0.
4
Rapid similarity searches of nucleic acid and protein data banks.核酸和蛋白质数据库的快速相似性搜索。
Proc Natl Acad Sci U S A. 1983 Feb;80(3):726-30. doi: 10.1073/pnas.80.3.726.
5
A computer program to enter DNA gel reading data into a computer.一个将DNA凝胶读数数据输入计算机的计算机程序。
Nucleic Acids Res. 1984 Jan 11;12(1 Pt 2):499-503. doi: 10.1093/nar/12.1part2.499.
6
A method for measuring the non-random bias of a codon usage table.一种测量密码子使用表非随机偏差的方法。
Nucleic Acids Res. 1984 Dec 21;12(24):9567-75. doi: 10.1093/nar/12.24.9567.
7
Measurements of the effects that coding for a protein has on a DNA sequence and their use for finding genes.蛋白质编码对DNA序列的影响的测量及其在寻找基因中的应用。
Nucleic Acids Res. 1984 Jan 11;12(1 Pt 2):551-67. doi: 10.1093/nar/12.1part2.551.
8
Nucleotide sequence of the lipoamide dehydrogenase gene of Escherichia coli K12.大肠杆菌K12硫辛酰胺脱氢酶基因的核苷酸序列。
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9
The pyruvate dehydrogenase complex of Escherichia coli K12. Nucleotide sequence encoding the dihydrolipoamide acetyltransferase component.大肠杆菌K12的丙酮酸脱氢酶复合体。编码二氢硫辛酰胺乙酰转移酶组分的核苷酸序列。
Eur J Biochem. 1983 Jul 1;133(3):481-9. doi: 10.1111/j.1432-1033.1983.tb07490.x.
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Complete nucleotide sequence of the chicken chromosomal ovalbumin gene and its biological significance.鸡染色体卵清蛋白基因的完整核苷酸序列及其生物学意义。
Biochemistry. 1981 Oct 27;20(22):6437-46. doi: 10.1021/bi00525a024.