BIGPROBE：一种能够高度可靠地预测长寡核苷酸探针序列的计算机程序。

BIGPROBE: a computer program that predicts the sequence of long oligonucleotide probes with high reliability.

作者信息

Dubnick M, Lewis L K, Mount D W

机构信息

Department of Molecular and Cellular Biology, University of Arizona, Tucson 85721.

出版信息

Nucleic Acids Res. 1988 Mar 11;16(5):1703-14. doi: 10.1093/nar/16.5.1703.

DOI:10.1093/nar/16.5.1703

原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC338165/

Abstract

We have written a computer program, BIGPROBE, which facilitates the design of long nucleic acid probes from the partial or complete amino acid sequence of a protein. BIGPROBE relies upon information on codon usage, intercodon dinucleotide frequency, and potential probe self-complementarity. We have examined the accuracy with which the program predicts coding sequences using sample human and rat genes and probe lengths of 30-60 nucleotides. Rat probe sequences selected by BIGPROBE using either codon usage or dinucleotide frequency data alone averaged 86-92% homology with the known exons of the corresponding gene sequences. Predictive accuracy with rat gene probes could be improved to 89-94%, depending upon probe length, by applying codon usage and dinucleotide frequency data in combination. Similar accuracy was achieved for human genes.

摘要

我们编写了一个计算机程序BIGPROBE，它有助于根据蛋白质的部分或完整氨基酸序列设计长核酸探针。BIGPROBE依赖于密码子使用情况、密码子间二核苷酸频率以及潜在探针自身互补性的信息。我们使用人类和大鼠的样本基因以及30至60个核苷酸的探针长度，检验了该程序预测编码序列的准确性。仅使用密码子使用情况或二核苷酸频率数据，由BIGPROBE选择的大鼠探针序列与相应基因序列的已知外显子平均具有86 - 92%的同源性。通过联合应用密码子使用情况和二核苷酸频率数据，根据探针长度不同，大鼠基因探针的预测准确性可提高到89 - 94%。对于人类基因也获得了类似的准确性。

相似文献

1

BIGPROBE: a computer program that predicts the sequence of long oligonucleotide probes with high reliability.BIGPROBE：一种能够高度可靠地预测长寡核苷酸探针序列的计算机程序。

Nucleic Acids Res. 1988 Mar 11;16(5):1703-14. doi: 10.1093/nar/16.5.1703.

2

SEQIN-ST and CODFREG: a full screen sequence editor and a codon usage analysis program for the Atari ST.SEQIN - ST和CODFREG：一款适用于雅达利ST计算机的全屏序列编辑器和密码子使用分析程序。

Nucleic Acids Res. 1988 Mar 11;16(5):1821-7. doi: 10.1093/nar/16.5.1821.

3

Computer selection of oligonucleotide probes from amino acid sequences for use in gene library screening.从氨基酸序列中进行计算机寡核苷酸探针选择以用于基因文库筛选。

Nucleic Acids Res. 1984 Jan 11;12(1 Pt 2):837-43. doi: 10.1093/nar/12.1part2.837.

4

Apple Macintosh programs for nucleic and protein sequence analyses.用于核酸和蛋白质序列分析的苹果麦金塔电脑程序。

Nucleic Acids Res. 1988 Mar 11;16(5):1837-46. doi: 10.1093/nar/16.5.1837.

5

Electronic fingerprinting of RNA.RNA的电子指纹识别

Nucleic Acids Res. 1988 Mar 11;16(5):1799-800. doi: 10.1093/nar/16.5.1799.

6

PROBFIND: a computer program for selecting oligonucleotide probes from peptide sequences.PROBFIND：一种从肽序列中选择寡核苷酸探针的计算机程序。

Nucleic Acids Res. 1986 Jan 10;14(1):567-70. doi: 10.1093/nar/14.1.567.

7

A computer program for the design of optimal synthetic oligonucleotide probes for protein coding genes.一种用于设计蛋白质编码基因最佳合成寡核苷酸探针的计算机程序。

Comput Appl Biosci. 1987 Nov;3(4):303-7. doi: 10.1093/bioinformatics/3.4.303.

8

'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.

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

Synthetic oligonucleotide probes deduced from amino acid sequence data. Theoretical and practical considerations.从氨基酸序列数据推导的合成寡核苷酸探针。理论与实践考量。

J Mol Biol. 1985 May 5;183(1):1-12. doi: 10.1016/0022-2836(85)90276-1.

引用本文的文献

1

Direct amplification of a single dissected chromosomal segment by polymerase chain reaction: a human brain sodium channel gene is on chromosome 2q22-q23.

Proc Natl Acad Sci U S A. 1991 Jan 15;88(2):335-9. doi: 10.1073/pnas.88.2.335.

本文引用的文献

1

Statistical characterization of nucleic acid sequence functional domains.核酸序列功能域的统计学特征

Nucleic Acids Res. 1983 Apr 11;11(7):2205-20. doi: 10.1093/nar/11.7.2205.

2

Isolation of a human anti-haemophilic factor IX cDNA clone using a unique 52-base synthetic oligonucleotide probe deduced from the amino acid sequence of bovine factor IX.利用从牛凝血因子IX氨基酸序列推导出来的一段独特的52个碱基的合成寡核苷酸探针分离人抗血友病因子IX cDNA克隆。

Nucleic Acids Res. 1983 Apr 25;11(8):2325-35. doi: 10.1093/nar/11.8.2325.

3

Isolation of a genomic clone for bovine pancreatic trypsin inhibitor by using a unique-sequence synthetic DNA probe.利用独特序列合成DNA探针分离牛胰蛋白酶抑制剂的基因组克隆。

Proc Natl Acad Sci U S A. 1983 Nov;80(22):6838-42. doi: 10.1073/pnas.80.22.6838.

4

Computer selection of oligonucleotide probes from amino acid sequences for use in gene library screening.从氨基酸序列中进行计算机寡核苷酸探针选择以用于基因文库筛选。

Nucleic Acids Res. 1984 Jan 11;12(1 Pt 2):837-43. doi: 10.1093/nar/12.1part2.837.

5

Computer programs used to aid in the selection of DNA hybridization probes.用于辅助选择DNA杂交探针的计算机程序。

Nucleic Acids Res. 1984 Jan 11;12(1 Pt 2):833-6. doi: 10.1093/nar/12.1part2.833.

6

Molecular cloning of a cDNA encoding human antihaemophilic factor.编码人抗血友病因子的cDNA的分子克隆

Nature. 1984;312(5992):342-7. doi: 10.1038/312342a0.

7

Expression of active human factor VIII from recombinant DNA clones.从重组DNA克隆中表达活性人凝血因子VIII。

Nature. 1984;312(5992):330-7. doi: 10.1038/312330a0.

8

Characterization of the human factor VIII gene.人类凝血因子VIII基因的特征分析。

Nature. 1984;312(5992):326-30. doi: 10.1038/312326a0.

9

Synthesis and use of synthetic oligonucleotides.合成寡核苷酸的合成与应用。

Annu Rev Biochem. 1984;53:323-56. doi: 10.1146/annurev.bi.53.070184.001543.

10

Isolation of the human insulin-like growth factor I gene using a single synthetic DNA probe.使用单一合成DNA探针分离人胰岛素样生长因子I基因。

EMBO J. 1984 Feb;3(2):361-4. doi: 10.1002/j.1460-2075.1984.tb01812.x.

文献AI研究员

20分钟写一篇综述，助力文献阅读效率提升50倍。

用中文搜PubMed

大模型驱动的PubMed中文搜索引擎

文档翻译

学术文献翻译模型，支持多种主流文档格式。