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In the present study, major constraints for codon and amino acid usage of Sulfolobus acidocaldarius, Sulfolobus solfataricus, Sulfolobus tokodali, Sulfolobus islandis and 6 other isolates from islandicus species of genus Sulfolobus were investigated. Correspondence analysis revealed high significant correlation between the major trend of synonymous codon usage and gene expression level, as assessed by the “Codon Adaptation Index” (CAI). There is a significant negative correlation between Nc (Effective number of codons) and CAI demonstrating role of codon bias as an important determinant of codon usage. The significant correlation between major trend of synonymous codon usage and GC3s (G + C at third synonymous position) indicated dominant role of mutational bias in codon usage pattern. The result was further supported from SCUO (synonymous codon usage order) analysis. The amino acid usage was found to be significantly influenced by aromaticity and hydrophobicity of proteins. However, translational selection which causes a preference for codons that are most rapidly translated by current tRNA with multiple copy numbers was not found to be highly dominating for all studied isolates. Notably, 26 codons that were found to be optimally used by genes of S. acidocaldarius at higher expression level and its comparative analysis with 9 other isolates may provide some useful clues for further in vivo genetic studies on this genus. 相似文献
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Blades MJ Ison JC Ranasinghe R Findlay JB 《Protein science : a publication of the Protein Society》2005,14(1):13-23
We identified key residues from the structural alignment of families of protein domains from SCOP which we represented in the form of sparse protein signatures. A signature-generating algorithm (SigGen) was developed and used to automatically identify key residues based on several structural and sequence-based criteria. The capacity of the signatures to detect related sequences from the SWISSPROT database was assessed by receiver operator characteristic (ROC) analysis and jack-knife testing. Test signatures for families from each of the main SCOP classes are described in relation to the quality of the structural alignments, the SigGen parameters used, and their diagnostic performance. We show that automatically generated signatures are potently diagnostic for their family (ROC50 scores typically >0.8), consistently outperform random signatures, and can identify sequence relationships in the "twilight zone" of protein sequence similarity (<40%). Signatures based on 15%-30% of alignment positions occurred most frequently among the best-performing signatures. When alignment quality is poor, sparser signatures perform better, whereas signatures generated from higher-quality alignments of fewer structures require more positions to be diagnostic. Our validation of signatures from the Globin family shows that when sequences from the structural alignment are removed and new signatures generated, the omitted sequences are still detected. The positions highlighted by the signature often correspond (alignment specificity >0.7) to the key positions in the original (non-jack-knifed) alignment. We discuss potential applications of sparse signatures in sequence annotation and homology modeling. 相似文献
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笔者撰写的“EMBOSS软件包序列分析程序实例”一文,已经在《生物信息学》期刊2021年第19卷第1期发表。此文介绍欧洲分子生物学开放软件包(European Molecular Biology Open Software Suite, EMBOSS)。EMBOSS是欧洲分子生物学网络组织(European Molecular Biology Network, EMBnet)于上世纪九十年代末启动的以欧洲国家为主的国际合作项目,是生物信息学领域中较早投入使用的大型开源软件包。本文基于笔者亲身经历,回顾EMBOSS项目的来龙去脉,讲述EMBnet三十多年来的发展历程,及其对生物信息开发、服务和教育培训等方面的贡献,从某个侧面为读者特别是年轻读者展示生物信息学发展早期的一段历史。 相似文献
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本文介绍欧洲分子生物学开放软件包EMBOSS序列分析程序应用实例。第1节简单介绍EMBOSS软件包的概况和基本用法。第2节介绍格式转换、序列提取、序列变换和序列显示等常用序列处理程序。第3节介绍序列比对程序,包括双序列比对、多序列比对和点阵图程序。第4节介绍常用核酸序列分析程序,可用于核苷酸组分统计、开放读码框分析、CpG岛识别、密码子使用统计和重复序列寻找等。第5节介绍常用蛋白质序列分析程序,包括氨基酸组分统计、序列特征位点识别、二级结构分析等。文中结合教学实例,选择部分常用程序,给出具体运行方式,并扼要说明分析结果的生物学意义。文末对程序运行过程中需要注意的地方加以讨论,并用表格列出部分常用程序的名称和用途,以便读者查阅。 相似文献
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