在超级计算机上进行序列搜索。

Sequence search on a supercomputer.

作者信息

Gotoh O, Tagashira Y

出版信息

Nucleic Acids Res. 1986 Jan 10;14(1):57-64. doi: 10.1093/nar/14.1.57.

DOI:10.1093/nar/14.1.57

原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC339355/

Abstract

A set of programs was developed for searching nucleic acid and protein sequence data bases for sequences similar to a given sequence. The programs, written in FORTRAN 77, were optimized for vector processing on a Hitachi S810-20 supercomputer. A search of a 500-residue protein sequence against the entire PIR data base Ver. 1.0 (1) (0.5 M residues) is carried out in a CPU time of 45 sec. About 4 min is required for an exhaustive search of a 1500-base nucleotide sequence against all mammalian sequences (1.2M bases) in Genbank Ver. 29.0. The CPU time is reduced to about a quarter with a faster version.

摘要

开发了一组程序，用于在核酸和蛋白质序列数据库中搜索与给定序列相似的序列。这些程序用FORTRAN 77编写，并针对日立S810 - 20超级计算机上的向量处理进行了优化。用45秒的CPU时间，可将一个500个残基的蛋白质序列与整个PIR数据库版本1.0（1）（0.5M个残基）进行比对搜索。在Genbank版本29.0中，用大约4分钟的时间可对一个1500个碱基的核苷酸序列与所有哺乳动物序列（120万个碱基）进行穷举搜索。使用更快的版本，CPU时间可减少到大约四分之一。

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本文引用的文献

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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

Identification of common molecular subsequences.常见分子子序列的鉴定

J Mol Biol. 1981 Mar 25;147(1):195-7. doi: 10.1016/0022-2836(81)90087-5.

3

An improved algorithm for matching biological sequences.一种用于匹配生物序列的改进算法。

J Mol Biol. 1982 Dec 15;162(3):705-8. doi: 10.1016/0022-2836(82)90398-9.

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.

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Gene product of v-fgr onc: hybrid protein containing a portion of actin and a tyrosine-specific protein kinase.v-fgr癌基因的基因产物：包含部分肌动蛋白和酪氨酸特异性蛋白激酶的杂合蛋白。

Science. 1984 Jan 6;223(4631):63-6. doi: 10.1126/science.6318314.

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Platelet-derived growth factor is structurally related to the putative transforming protein p28sis of simian sarcoma virus.血小板衍生生长因子在结构上与猿猴肉瘤病毒假定的转化蛋白p28sis相关。

Nature. 1983;304(5921):35-9. doi: 10.1038/304035a0.

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Nucleotide sequence and expression of an AIDS-associated retrovirus (ARV-2).一种艾滋病相关逆转录病毒（ARV-2）的核苷酸序列与表达

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