一种用于蛋白质相似性分析的新的相对距离

本文论述了一种新的相对距离,用于分析不同蛋白质序列的相似性分析和构造进化树．此种距离基于Lempel-Zip复杂度,不需要进行序列比对和复杂性算法．为了说明这种距离的合理性,本文对8个物种进行了相似性分析并构造了其进化树．     

Phylogenetic analysis of DNA sequences based on the generalized pseudo-amino acid composition

The main work of this paper is to propose a new theory and method, which is based on the idea of the pseudo-amino acid composition, for phylogenetic analysis of DNA primary sequences. In our method, we revise the part of the occurrence frequency of 20 amino acids in the method of the pseudo-amino acid composition by replacing the frequency of 16 dinucleotides. And we select eight LZ complexity factors of eight (0,1) sequences of a DNA primary sequence as PseAA components. Finally, we characterize a DNA sequence with a 24-dimensional vector. We reconstruct the phylogenetic trees of two datasets. The results show that our method is efficient and significant.     

A weighted measure for the similarity analysis of DNA sequences

Here we propose a weighted measure for the similarity analysis of DNA sequences. It is based on LZ complexity and (0,1) characteristic sequences of DNA sequences. This weighted measure enables biologists to extract similarity information from biological sequences according to their requirements. For example, by this weighted measure, one can obtain either the full similarity information or a similarity analysis from a given biological aspect. Moreover, the length of DNA sequence is not problematic. The application of the weighted measure to the similarity analysis of β-globin genes from nine species shows its flexibility.     

mtDNA基因树拓扑距离比较和基因分群

基因树间拓扑距离数据的比较进一步证明：与分割拓扑距离相比,能经拓扑距离是一种更为精确的测度,利用相对通经拓扑距离构建了8个基因的拓扑距离树。基因的拓扑距离树能直观地反映不同基因树的拓扑结构差异大小,可用来对基因进行分群。此外,发现不同DNA序列用于构建多基因树中其系统发生信息存在“累加”,“合取”,“含盖”,“相斥”等数学关系。这可解释在mtDNA基因组中一些基因比另一些基因更适合用来的构建树的结果。结果提示从GenBank中应选择具有累加基因的DNA序列或蛋白质氨基酸序列合并来构建物种。在讨论中还提出了一种获得真树的新建树策略。     

云锦杜鹃NRT基因序列的生物信息学分析

通过转录组测序,获得在接种 ERM 真菌的云锦杜鹃苗根系中显著差异表达的基因,其中硝酸根转运蛋白(NRT )基因是硝态氮吸收转运的关键基因。利用生物信息学方法,分析云锦杜鹃根转录组的硝酸根转运蛋白(NRT )基因序列,对其推导的氨基酸的理化性质、亲水性/疏水性、跨膜结构、导肽、二级结构、高级结构进行预测,并对硝酸根转运蛋白的氨基酸做进化发育分析。为进一步了解 NRT 基因在云锦杜鹃接种苗根系氮素吸收的作用奠定了基础。     

中国几种剧毒鹅膏菌的ITS序列分析

测定了来自中国不同地区的9个剧毒鹅膏菌的核糖体内转录间隔区(ITS)核苷酸序列.以湖南鹅膏为外类群,用ITS序列构建了系统进化树.结果表明:两个不同产地的欧氏鹅膏存在一定的差异,但仍可聚为同一组;欧氏鹅膏与其它几种剧毒鹅膏的亲缘关系较远;两个根据形态特征鉴定为灰花纹鹅膏的标本可能是两个不同的种;欧氏鹅膏、致命鹅膏和黄盖鹅膏白色变种这3个产生白色子实体的种系统演化上不是同源的.     

昆虫血清素受体蛋白的生物信息学分析

【目的】昆虫血清素(5-羟色胺)受体已知有5个亚型。本文旨在系统分析昆虫5-羟色胺受体亚型蛋白的结构和进化关系。【方法】首先对文献报道已明确亚型7种昆虫的5-羟色胺受体(23个亚型序列)进行生物信息学分析,然后采用多序列比对和进化树构建的方法对NCBI数据库中推测可能为昆虫5-羟色胺受体蛋白序列进行分析。【结果】发现47个推测是昆虫5-羟色胺受体的蛋白序列中,有40个蛋白序列属于昆虫5-羟色胺受体,其余7个未能确认的昆虫5-羟色胺受体的蛋白序列都具有7个跨膜区域,属于G蛋白偶联受体家族,但不一定为5-羟色胺受体。【结论】本文对昆虫5-羟色胺受体蛋白的系统进化树分析,间接地证明了本文确认的昆虫5-羟色胺受体亚型注释信息的准确性,发现分类上同属一个目的昆虫5-HT受体序列的亲缘性较近。本研究为昆虫5-羟色胺受体的结构和功能分析提供基础。     

链格孢属小孢子种的RAPD分析

用筛选出的12个随机引物,对链格孢属Alternaria13个小孢子种和作为对照的3个大孢子种共55个分离系(isolates)进行RAPD分析。大孢子种Alternariasolani、A.porri和形态独特的A.leucanthemi在树状聚类图上遗传距离0.44处与所有供试小孢子种区分开,它们彼此之间在遗传距离0.25处相区分,表明所采用的RAPD分析方法适于链格孢种间亲缘关系的研究。所有供试的链格孢小孢子种在遗传距离0.31水平上被聚在一起,表明它们之间的亲缘关系较近。A.infectoria与其它链格孢小孢子种之间遗传距离较远;A.longipes的3个分离系和A.brassicicola的7个分离系在较低的遗传距离上被聚在一起,表明它们是独立的种。其它供试链格孢小孢子种的不同分离系在树状聚类图上未显示明确区分。     

链格孢属小孢子种的RAPD分析*

用筛选出的12个随机引物,对链格孢属Alternaria13个小孢子种和作为对照的3个大孢子种共55个分离系(isolates)进行RAPD分析。大孢子种Alternariasolani、A.porri和形态独特的A.leucanthemi在树状聚类图上遗传距离0.44处与所有供试小孢子种区分开,它们彼此之间在遗传距离0.25处相区分,表明所采用的RAPD分析方法适于链格孢种间亲缘关系的研究。所有供试的链格孢小孢子种在遗传距离0.31水平上被聚在一起,表明它们之间的亲缘关系较近。A.infectoria与其它链格孢小孢子种之间遗传距离较远;A.longipes的3个分离系和A.brassicicola的7个分离系在较低的遗传距离上被聚在一起,表明它们是独立的种。其它供试链格孢小孢子种的不同分离系在树状聚类图上未显示明确区分。     

Whole genome-based phylogenetic analysis of bacterial two-component systems

To adapt to their environment, bacterial strains have developed various environmental signal sensing systems or twocomponent systems. To evaluate the evolutionary relationship of two-component systems, 246 two-component system genes from KEGG were analyzed. Phylogenetic tree structure indicated that most two-component systems are strain specific. Most of two-component system genes have co-evolved, and some two-component system pairs have evolved via recruitment model. By two-component system gene content analysis, new aspect of cellular metabolism evolution was provided.     

Heads or tails: a simple reliability check for multiple sequence alignments

The question of multiple sequence alignment quality has received much attention from developers of alignment methods. Less forthcoming, however, are practical measures for addressing alignment quality issues in real life settings. Here, we present a simple methodology to help identify and quantify the uncertainties in multiple sequence alignments and their effects on subsequent analyses. The proposed methodology is based upon the a priori expectation that sequence alignment results should be independent of the orientation of the input sequences. Thus, for totally unambiguous cases, reversing residue order prior to alignment should yield an exact reversed alignment of that obtained by using the unreversed sequences. Such "ideal" alignments, however, are the exception in real life settings, and the two alignments, which we term the heads and tails alignments, are usually different to a greater or lesser degree. The degree of agreement or discrepancy between these two alignments may be used to assess the reliability of the sequence alignment. Furthermore, any alignment dependent sequence analysis protocol can be carried out separately for each of the two alignments, and the two sets of results may be compared with each other, providing us with valuable information regarding the robustness of the whole analytical process. The heads-or-tails (HoT) methodology can be easily implemented for any choice of alignment method and for any subsequent analytical protocol. We demonstrate the utility of HoT for phylogenetic reconstruction for the case of 130 sequences belonging to the chemoreceptor superfamily in Drosophila melanogaster, and by analysis of the BaliBASE alignment database. Surprisingly, Neighbor-Joining methods of phylogenetic reconstruction turned out to be less affected by alignment errors than maximum likelihood and Bayesian methods.     

Phylogenetic information improves homology detection.

We present a database search method that is based on phylogenetic trees (treesearch). The method is used to search a protein sequence database for homologs to a protein family. In preparation for the search, a phylogenetic tree is constructed from a given multiple alignment of the family. During the search, each database sequence is temporarily inserted into the tree, thus adding a new edge to the tree. Homology between family and sequence is then judged from the length of this edge. In a comparison of our method to profiles (ISREC pfsearch), two implementations of hidden Markov models (HMMER hmmsearch and SAM hmmscore), and to the family pairwise search (FPS) method on 43 families from the SCOP database based on minimum false-positive counts (min-FPCs), we found a considerable gain in sensitivity. In 69% of the test cases, treesearch showed a min-FPC of at most 50, whereas the two second best methods (hmmsearch and FPS) showed this performance only in 53% cases. A similar impression holds for a large range of min-FPC thresholds. The results demonstrate that phylogenetic information can significantly improve the detection of distant homologies and justify our method as a useful alternative to existing methods.     

汉滩病毒M片段的核苷酸序列变异和系统发生树分析

The total RNA was extracted from two clinical blood samples of HFRS patients and the RNA was amplified by RT-PCRThe amplified DNA fragment of sample 613 involved nucleotides 1,471-1,873,and the sample 226 involved 540-1,244 nucleotides of M fragment of Hantaan virusThen the amplified PCR products were sequenced directlyThe sequencing results demonstrated that there was 84% identity between sample 613 and HV114 virus strain,but was 99% between sample 613 and HTN76-118 strainHowever,in sample 226,there was 95% sequence identity with HV114,82% with HTN76-118The results of phylogenetic tree analysis showed that HV613 was located in the same linage with HTN76-118,the HV226 was in the same linage with HV114 and A9 strains     

猴类pERT87-15位点的多态性分析

应用人X染色体上的pERT87-15DNA探针,分析了猕猴属的猕猴、豚尾猕猴、熊猴、毛面短尾猴和红面短尾猴等共5种89只猴子的基因组DNA,首次发现在相当于人类 pERT87-15的位点上存在着3个“等距”的多态性位点。单体型分析提示这3个多态位点位于其X染色体上。这些结果表明,人类某些基因组探针也可适用于某些灵长类动物基因组DNA的多态性分析,并为研究动物DNA及其种系发生提供了新的信息。     

Prokaryote phylogeny based on ribosomal proteins and aminoacyl tRNA synthetases by using the compositional distance approach

In order to show that the newly developed K-string composition distance method, based on counting oligopeptide frequencies, for inferring phylogenetic relations of prokaryotes works equally well without requiring the whole proteome data, we used all ribosomal proteins and the set of aminoacyl tRNA synthetases for each species. The latter group has been known to yield inconsistent trees if used individually. Our trees are obtained without making any sequence alignment. Altogether 16 Archaea, 105 Bacteria and 2 Eucarya are represented on the tree. Most of the lower branchings agree well with the latest, 2003, Outline of the second edition of the Bergey’s Manual of Systematic Bacteriology and the trees also suggest some relationships among higher taxa.     

墨天牛属昆虫COⅠ基因比较及系统学初步研究

【目的】对11种墨天牛线粒体DNA细胞色素氧化酶C亚基Ⅰ基因(COⅠ)进行比较并对墨天牛属系统发育关系进行初步探讨。【方法】本文测定分析了11种墨天牛线粒体DNA细胞色素氧化酶C亚基Ⅰ基因(COⅠ),并采用简约法和贝叶斯推论法构建了墨天牛属的分子进化树。【结果】序列比对分析得到470 bp大小的COⅠ基因片段,其中可变异位点169个(36.0%),保守位点301个(64.0%),转换/颠换的平均值(R值)为1.03,说明此段序列适合于分子进化树。利用不同系统发育重建方法得到的进化树具有相似的拓扑结构,同时结合形态学分类特征对墨天牛属昆虫的分子系统进化关系进行探讨。结果显示分子结果与形态分类结果相似。【结论】利用COⅠ基因构建的墨天牛属系统发育树是探讨墨天牛分类的有效方法。     

DNA似近距离及进化时间的估算

在似近分析和Ｎｅｉ氏遗传距离的基础上,给出了ＤＮＡ似近距离计算公式,并以ＤＮＡ似近距离估算类群间的分歧时间（进化时间）,应用１０种限制内切酶对猕猴属（ｇｅｎｕｓ Ｍａｃａｃａ）内５个种ｍｔＤＮＡ的切点数据计算了这５个种的ＤＮＡ似近距离和进化时间,比较由ＤＮＡ似近距,遗传距离构建的歧化树和Ｆｏｏｄｅｎ及Ｄｅｌｓｏｎ的形态歧化树表明,除遗传距离的歧化树外,其它三种歧化树都有一个共同点,就是熊猴（Ｍ．ａ