一个生物网络比对的启发式算法

随着各种高通量生物实验技术的发明和广泛应用,越来越多的分子生物网络数据被公布.有效而且可靠的比对这些网络对检测分子生物网络的保守性功能模块和推测物种间的进化关系有着十分重要的意义.然而,由于网络比对在理论上是NP-困难（nondeterministic polynomialtime-hard）问题,它已经成为当前计算生物学需要攻克的主要难点之一.本文提出了一个比对两个蛋白质相互作用网络的启发式算法.该算法首先通过比较两个网络中所有顶点的邻域相似性给出这两个网络的顶点相似性矩阵,然后利用该矩阵将全局网络比对问题转化为一个二部图匹配问题.众所周知,二部图匹配问题具有多项式时间复杂度算法,本文利用ILOG CPLEX软件进行求解.为了验证该算法的优越性,作者比对了水痘病毒（varicella-zoster,VZV）和卡波济（氏）肉瘤病毒（kaposi＇s sarcomaassociated herpesvirus,KSHV）的蛋白质相互作用网络,并且把比对结果同其它网络比对算法进行比较.结果证明该算法显著提高了全局网络比对的精确度.     

一个新的多序列比对算法

多序列比对是生物信息学中基础而又重要的序列分析方法.本文提出一种新的多序列比对算法,该算法综合了渐进比对方法和迭代策略,采用加权函数以调整序列的有偏分布,用neighbor-joining方法构建指导树以确定渐进比对的顺序.通过对BAlibASE中142组蛋白质序列比对的测试,验证了本算法的有效性.与Multalin算法比较的结果表明,本算法能有效地提高分歧较大序列的比对准确率.     

基于Progressive多序列比对方法的求解多序列比对的启发式算法

在生物信息学研究中,生物序列比对问题占有重要的地位。多序列比对问题是一个NPC问题,由于时间和空间的限制不能够求出精确解。文中简要介绍了Feng和Doolittle提出的多序列比对算法的基本思想,并改进了该算法使之具有更好的比对精度。实验结果表明,新算法对解决一般的progressive多序列比对方法中遇到的局部最优问题有较好的效果。     

一个新的核酸序列比对算法及其在序列全局比对中的应用

目前在序列比对中所广泛使用的动态规划算法,虽然能达到最优比对结果,但却由于具有高计算复杂度O(N_2)而极大地降低了计算效率。将多阶段动态规划决策算法用于两两序列比对并用Visual BASIC编程实现,结果发现该新算法在将计算复杂度减小到O(N)的同时,也能够获得较为理想的计算精度,预期将在序列全局比对中起重要作用。     

整体蛋白质电喷雾质谱原位解析

蛋白质组学系统研究了生物体蛋白质组,尤其是一定生理、病理条件下差异表达的蛋白;对蛋白质序列、翻译后修饰及其位置的定性鉴定可以帮助我们系统地了解蛋白质的结构和功能。随着软电离技术(如电喷雾电离技术)及高质量测量精度、高质量分辨质谱仪(如轨道阱质谱仪)的发展与相对普及,完整蛋白质的质谱表征(即所谓的自上而下蛋白质组学)已成为可能且渐渐流行起来;相应的数据库搜索引擎和蛋白质鉴定生物信息学工具也有了一定的进展。本文对作者研发的蛋白质电喷雾质谱原位解析算法"同位素质荷比及轮廓指纹比对"及整体蛋白质数据库搜索引擎"Protein Goggle2.0"(http://proteingoggle.tongji.edu.cn/)做一个概述。     

一类蛋白质相互作用网络比对的线性规划算法

随着越来越多的蛋白质相互作用数据被公布，网络比对在预测蛋白质的新功能和推测蛋白质网络进化历史上发挥着越来越重要的作用。但是，目前主要的网络比对方法要么忽略蛋白质的同源信息或蛋白质网络的结构信息，要么采用启发式算法。文章作者通过将网络比对转化为线性规划问题给出了一个精确的网络比对算法，并且针对水痘病毒和卡波济(氏)肉瘤病毒的蛋白质相互作用数据进行了比对分析。     

多序列比对算法的研究进展

多序列比对在阐明一组相关序列的重要生物学模式方面起着十分重要的作用。自从计算机的出现,就有许多研究者致力于多序列比对算法。人类基因组计划和单体型计划使多序列比对研究再次成为研究热点。本文详细归纳了多序列比对的主要算法,总结了国内外近年来多序列比对的研究进展,同时也分析并预测了未来该问题的研究方向。     

基于Yarn云平台的生物基因多序列比对并行算法

为了解决生物信息学中基因多序列比对的计算速度慢和软件陈旧的问题,提出了基于Yarn(Yet Another Resource Negotiator)云平台的生物基因多序列比对并行计算方法Yarn_clustalW。分析了clustalW算法的数学模型及其面向MapReduce的任务划分方式,Yarn_clustalW中综合考虑了基因的长度和数目,采用一种基于阈值刻度的任务划分方式。利用NCBI的GenBank生物基因数据作为案例程序进行了测试。实验结果表明:Yarn_clustalW比起多序列比对clustalW串行计算方法具有更快的运行时间与加速比,可以使生物科研人员节省很多时间与精力,方便对于药物靶标的发现,缩短生物药物的开发周期。     

基于堆积协变信息与最小自由能预测含伪结的RNA二级结构

RNA伪结预测是RNA研究的一个难点问题。文中提出一种基于堆积协变信息与最小自由能的RNA伪结预测方法。该方法使用已知结构的RNA比对序列(ClustalW比对和结构比对)测试此方法, 侧重考虑相邻碱基对之间相互作用形成的堆积协变信息, 并结合最小自由能方法对碱基配对综合评分, 通过逐步迭代求得含伪结的RNA二级结构。结果表明, 此方法能正确预测伪结, 其平均敏感性和特异性优于参考算法, 并且结构比对的预测性能比ClustalW比对的预测性能更加稳定。文中同时讨论了不同协变信息权重因子对预测性能的影响, 发现权重因子比值在l1: l2=5:1时, 预测性能达到最优。     

基于堆积协变信息与最小自由能预测含伪结的RNA二级结构

RNA伪结预测是RNA研究的一个难点问题。文中提出一种基于堆积协变信息与最小自由能的RNA伪结预测方法。该方法使用已知结构的RNA比对序列(ClustalW比对和结构比对)测试此方法, 侧重考虑相邻碱基对之间相互作用形成的堆积协变信息, 并结合最小自由能方法对碱基配对综合评分, 通过逐步迭代求得含伪结的RNA二级结构。结果表明, 此方法能正确预测伪结, 其平均敏感性和特异性优于参考算法, 并且结构比对的预测性能比ClustalW比对的预测性能更加稳定。文中同时讨论了不同协变信息权重因子对预测性能的影响, 发现权重因子比值在l1: l2=5:1时, 预测性能达到最优。     

Historical stocking data and 19th century DNA reveal human‐induced changes to native diversity and distribution of cutthroat trout

Many species are threatened with extinction and efforts are underway worldwide to restore imperilled species to their native ranges. Restoration requires knowledge of species' historical diversity and distribution. For some species, many populations were extirpated or individuals moved beyond their native range before native diversity and distribution were documented, resulting in a lack of accurate information for establishing restoration goals. Moreover, traditional taxonomic assessments often failed to accurately capture phylogenetic diversity. We illustrate a general approach for estimating regional native diversity and distribution for cutthroat trout in the Southern Rocky Mountains. We assembled a large archive of historical records documenting human‐mediated change in the distribution of cutthroat trout (Oncorhynchus clarkii) and combined these data with phylogenetic analysis of 19th century samples from museums collected prior to trout stocking activities and contemporary DNA samples. Our study of the trout in the Southern Rocky Mountains uncovered six divergent lineages, two of which went extinct, probably in the early 20th century. A third lineage, previously declared extinct, was discovered surviving in a single stream outside of its native range. Comparison of the historical and modern distributions with stocking records revealed that the current distribution of trout largely reflects intensive stocking early in the late 19th and early 20th century from two phylogenetically and geographically distinct sources. Our documentation of recent extinctions, undescribed lineages, errors in taxonomy and dramatic range changes induced by human movement of fish underscores the importance of the historical record when developing and implementing conservation plans for threatened and endangered species.     

The Austral floristic realm revisited

The classification of the Earth's flora into floristic regions has been the major goal of plant geography since the 19th century. A detailed revision of 19th and 20th century classifications is presented herein, with particular emphasis on the delimitation of the Austral floristic realm. A comparison between Chile, New Zealand, and the Cape Floristic Region is made at the genus level. Using the vascular flora of these biogeographical regions, the analysis revises previous attempts to define the Austral realm, while also assessing differences made by changes in taxonomic delimitations from recent molecular phylogenetic studies. The results indicate that the Austral floristic realm can nowadays be better described as a circum-Antarctic generalized track, composed of some 60 genera and 15 families restricted to South America and Australasia, possibly including South Africa.     

Nucleotide triplet based molecular phylogeny of class I and class II aminoacyl t-RNA synthetase in three domain of life process: bacteria, archaea, and eukarya

The aminoacyl-tRNA synthetases are one of the major protein components in the translation machinery. These essential proteins are found in all forms of life and are responsible for charging their cognate tRNAs with the correct amino acid. These important enzymes have been the subject of intense scientific inquiry for nearly half a century, but their complete evolutionary history has yet to emerge. Amino acids sequence based phylogeny has some limitation due to very low sequence similarity amongst the different tRNA synthetases and structure based phylogeny has also its limitation. In our study, tRNA nucleotide sequences of E. coli K12 (Bacteria), Saccharomyces cerevisiae (Eukarya), Thermococcus kodakaraensis KOD1, and Archaeoglobus fulgidus DSM 4304 (Archaea) were used for phylogenetic analysis. Our results complement the observation with the earlier studies based on multiple sequence alignment and structural alignment. We observed that relationship between archaeal tRNA synthetases are different that of bacteria and eucarya. Violation of Class rule of LysRS is observed here also. The uniqueness of this method is that it does not employ sequence alignment of complete nucleotide sequence of the corresponding gene.     

The impact of multiple protein sequence alignment on phylogenetic estimation

Multiple sequence alignment is typically the first step in estimating phylogenetic trees, with the assumption being that as alignments improve, so will phylogenetic reconstructions. Over the last decade or so, new multiple sequence alignment methods have been developed to improve comparative analyses of protein structure, but these new methods have not been typically used in phylogenetic analyses. In this paper, we report on a simulation study that we performed to evaluate the consequences of using these new multiple sequence alignment methods in terms of the resultant phylogenetic reconstruction. We find that while alignment accuracy is positively correlated with phylogenetic accuracy, the amount of improvement in phylogenetic estimation that results from an improved alignment can range from quite small to substantial. We observe that phylogenetic accuracy is most highly correlated with alignment accuracy when sequences are most difficult to align, and that variation in alignment accuracy can have little impact on phylogenetic accuracy when alignment error rates are generally low. We discuss these observations and implications for future work.     

Les reconstructions phylogénétiques dans les Annales de Paléontologie (1906-1950). Comparaison avec d'autres revues françaises

A systematic examination of the three major French periodicals which published the majority of paleontological papers in the first part of the 20th century shows that phylogenetic conjectures were rare, in contrast with other countries in the same period. The three journals are compared from the point of view of the number and the nature of the figures that represented phylogenies. The evolution of these figures is also considered. We show that the Annales de paléontologie shared the same attitude as the other journals: a general tendency towards increased methodological cautiousness is observed, with special regards to stratigraphic standards. The results of the inquiry are interpreted in the light of the professional structure of French palaeontology in the first half of the 20th Century.     

系统发育研究中多重序列比对常见问题分析

在简单介绍序列比对原理的基础上,结合自己的经验,对经常出现的问题进行总结分析,以期在将来的序列比对工作中避免此类问题的发生.     

The Not-so-Dark Ages: ecology for human growth in medieval and early twentieth century Portugal as inferred from skeletal growth profiles

This study attempts to address the issue of relative living standards in Portuguese medieval and early 20th century periods. Since the growth of children provides a good measure of environmental quality for the overall population, the skeletal growth profiles of medieval Leiria and early 20th century Lisbon were compared. Results show that growth in femur length of medieval children did not differ significantly from that of early 20th century children, but after puberty medieval adolescents seem to have recovered, as they have significantly longer femora as adults. This is suggestive of greater potential for catch-up growth in medieval adolescents. We suggest that this results from distinct child labor practices, which impact differentially on the growth of Leiria and Lisbon adolescents. Work for medieval children and adolescents were related to family activities, and care and attention were provided by family members. Conversely, in early 20th century Lisbon children were more often sent to factories at around 12 years of age as an extra source of family income, where they were exploited for their labor. Since medieval and early 20th century children were stunted at an early age, greater potential for catch-up growth in medieval adolescents results from exhausting work being added to modern adolescent's burdens of disease and poor diet, when they entered the labor market. Although early 20th century Lisbon did not differ in overall unfavorable living conditions from medieval Leiria, after puberty different child labor practices may have placed modern adolescents at greater risk of undernutrition and poor growth.     

Spidermonkey: rapid detection of co-evolving sites using Bayesian graphical models

Spidermonkey is a new component of the Datamonkey suite of phylogenetic tools that provides methods for detecting coevolving sites from a multiple alignment of homologous nucleotide or amino acid sequences. It reconstructs the substitution history of the alignment by maximum likelihood-based phylogenetic methods, and then analyzes the joint distribution of substitution events using Bayesian graphical models to identify significant associations among sites. AVAILABILITY: Spidermonkey is publicly available both as a web application at http://www.data-monkey.org and as a stand-alone component of the phylogenetic software package HyPhy, which is freely distributed on the web (http://www.hyphy.org) as precompiled binaries and open source.     

基于COⅠ和Cyt b基因序列的凤蝶科六属分子系统学研究

对凤蝶科6属25种的COⅠ基因和20种Cyt b基因的部分序列进行测定和分析, 探讨它们之间的系统发育关系; 以茶小卷叶蛾Adoxophyes honmai为外群, 用邻接法(neighbor-joining, NJ)、 最大简约法(maximum parsimony, MP)和贝叶斯法(Bayesian inference, BI)重建了凤蝶科6属的分子系统树。结果表明： COⅠ基因部分序列长度为661 bp, 其中保守位点417个, 可变位点244个, 简约信息位点191个; A+T的平均含量为70.3%, 明显高于C+G的平均含量29.6%。Cyt b基因部分序列长度为433 bp, 其中保守位点239个, 可变位点194个, 简约信息位点135个; A+T的平均含量为74.2%, 明显高于C+G的平均含量25.7%。分子系统树表明, 凤蝶属Papilio、 斑凤蝶属Chilasa、 尾凤蝶属Bhutanitis、 珠凤蝶属Pachliopta和喙凤蝶属Teinopalpus为单系性, 与传统形态分类结果相一致。但青凤蝶属Graphium单系性不够明确, 需要进一步探讨。研究结果为我国凤蝶科分子系统学研究积累了资料。