RNA 结构预测工具 PPfold 3.0 熊荣川 译 六盘水师范学院生物信息学实验室 xiongrongchuan@126.com http://blog.sciencenet.cn/u/Bearjazz 随着物理方法测定的 RNA 结构数据越来越丰富，以及 RNA 初级、高级结构之间关系研究的深入，现在涌现出一大批基于系统发生和已有 RNA 结构数据库来预测未知 RNA 结构的生物信息学方法，相应也产生了学多软件工具，下面简单的介绍其中一款软件 PPfold 3.0 。 PPfold 3.0 一款基于 Pfold 算法的 RNA 二级结构预测工具软件，是 PPfold 的升级，更丰富了既有 RNA 结构的参考和算法的优化。该软件为 java 程序，不依赖任何操作系统，可以到以下地址下载安装使用。 http://birc.au.dk/software/ppfold. 原文： PPfold 3.0: Fast RNA secondary structure prediction using phylogeny and auxiliary data Zsuzsanna S¨uk¨osd 1 ; 2 ; 3 _ , Bjarne Knudsen 4 , Jrgen Kjems 1 ; 2 , and Christian NS Pedersen 3 ; 5 ABSTRACT PPfold is a multithreaded implementation of the Pfold algorithm for RNA secondary structure prediction. Here we present a new version of PPfold, which extends the evolutionary analysis with a exible probabilistic model for incorporating auxiliary data, such as data from structure probing experiments. Our tests show that the accuracy of single-sequence secondary structure prediction using experimental data in PPfold 3.0 is comparable to RNAstructure. Furthermore, alignment structure prediction quality is improved even further by the addition of experimental data. PPfold 3.0 therefore has the potential of producing more accurate predictions than it was previously possible. Availability and Implementation PPfold 3.0 is available as a platform-independent Java application, and can be downloaded from http://birc.au.dk/software/ppfold. Contact Zsuzsanna S¨uk¨osd, zs@birc.au.dk.
【论文阅读笔记，Leiting, Jun 27, 2012】 A decade of web server updates at the bioinformatics links directory: 2003–2012 Nucl. Acids Res. (2012) 40 (W1): W3-W12. doi: 10.1093/nar/gks632 因为数量的大量增加，对于生物信息学的研究人员来说，跟踪生物信息学工具和数据库变得越来越困难，因此，根据内容和用途建立一个生物信息学算法、数据库和文献的索引变得越来越重要。 而 Bioinformatics Links Directory 的建立便是用于解决这个问题。这个目录收集了序列资源(Molecular resources)、工具和数据库的链接，并分成了 11 个大类，和若干小类，共 134 个资源 (Resources)，455 个数据库 (Databases)，和 1205 个网络服务器工具 (Web server tools)。 11 个大类是： Computer Related DNA Education Expression Human Genome Literature Model Organisms Other Modules Protein RNA Sequence Comparison
晶体结构数据工具网页 http://www.cryst.ehu.es/ 包括用对称群给出原子坐标（ WYCKPOS Wyckoff Positions of Space Groups ）， 布里渊区高对称点（ KVEC The k-vector types and Brillouin zones of Space Groups ）， 等数据库。
来源 1 http://emuch.net/bbs/viewthread.php?tid=3748553 1.StyleWriter （润色首推） 嵌入 word 使用。主要功能：检查拼写、语法等错误，润色文章。 本软件的诱人之处在于润色文章，可以有提示你对同义词做选择，让你的文章更地道。 http://www.editorsoftware.com/downloads/DWSWT.html 另外还有统计文章特征的功能，详见李泳老师的博文：从 Stylewriter 看英文写作 2.Triivi （检查首选） 英文输入软件，免费开源，具备词频调整、智能纠错，根据已经输入的字母猜出想写点词或短语，提高英文输入速度！标准版具有 50 万词汇量 , 专业词库 ( 约 20 万词汇 ). http://www.triivi.com/ 3.Intellicomplete( 推荐 ) 虽没有 triivi 专业词汇丰富，但定义性较强，且自定义语库方便，只需要一个快捷键 Ctrl+Alt+J 。 http://www.download.com/IntelliComplete/3000-2079_4-10062169.html 4.As-U-Type 是一款英文输入单词自动校正软件，根据软件自带的和自定义的校正词典，当你编辑文档输入的单词有误是，它会自动帮你校正。 此软件是在输入后按空格键后给出提示，没有实时提醒功能，这个很遗憾。 http://www.asutype.com/files/asutype-setup.exe 5.TypeTip 与 As-U-Type 功能雷同的辅助录入软件，具有实时提示及校正功能，但不能输入词组 phrase, 不过兼容性较好。 http://www.sharewareconnection.com/typetip.htm 6. 金山写作助手 金山词霸自带工具。编写英文文档时，常常会遭遇当前语境不知该用哪个单词的尴尬，这时你会怎么办？打开词霸查找一通？哦，那太麻烦了。其实最简单的方法，是快速按动两下 Alt 键。这时词霸将自动弹出一个特别设计的 “ 写作助手 ” 模块，试着输入一下中文词汇吧。看到了吗？软件将自动弹出一组与搜索词对应的英文单词，如果感觉片面的解释无法帮助判断，还可以继续输入一个 “ 分号 ” ，这时 “ 写作助手 ” 将会在翻译结果中自动加入精选例句。 7.Bullfighter 可用作微软 Word 和 PowerPoint 的插件 ( www.fightthebull.com/bullfighter.asp) ，不过它只能在 Windows 操作系统中运行。 Bullfighter 的目标是找到并且删除你文章中那些难懂的部分。 8.whitesomke, WriteExperss 虽然 WhiteSmoke 也向中国和印度的母语非英语者推销这款产品，但公司表示他们最大的目标客户群仍是那些想让自己的文笔变得典雅一些的以英语为母语者。 http://www.jz5u.com/Soft/teach/waiyu/13557.html 来源 2 http://emuch.net/bbs/viewthread.php?tid=3669411 各位虫友们，各位科研工作者们大家好，对于大家来说成果最后都是要通过文章来表现出来，为了让更多的人了解自己的成果，所以科研论文写作，尤其是外文科研论文的写作显得尤为重要。下面由我向大家推荐本版关于论文写作的一些优秀的帖子，其中包括中外大牛或大数据库机构对论文写作的经验和建议。 1 ，首先是国外的一些大牛们的宝贵的经验和建议，帖子如下： 【教程】大牛教你写论文（哈佛大学）； http://emuch.net/bbs/viewthread.php?tid=3514631fpage=1 【素材】从科研到写作（国外教授教你如何写论文）； http://emuch.net/bbs/viewthread.php?tid=3484927fpage=1 【课件】如何写科技论文（哈佛大学）； http://emuch.net/bbs/viewthread.php?tid=3390211fpage=1 【素材】如何写论文（剑桥大学）； http://emuch.net/bbs/viewthread.php?tid=3572060fpage=1 2 ，接下来是一些著名的论坛和数据库们的经验和建议，帖子如下： 【教程】 Secrets to Writing Better Scientific Articles （ ACP ）； http://emuch.net/bbs/viewthread.php?tid=3665940fpage=1 【素材】 Paper 论文实用手册（上海交大 BBS ）； http://emuch.net/bbs/viewthread.php?tid=3663948fpage=1 【课件】 Writing for Success ； http://emuch.net/bbs/viewthread.php?tid=3227958fpage=2 3 ，然后就是一些关于论文写作的分步解析和常见问题解析，帖子如下： 【课件】如何写好一篇 SCI 论文的题名 SCI 高被引论文题名分析； http://emuch.net/bbs/viewthread.php?tid=3437674fpage=1 【素材】科技论文写作分步解析； http://emuch.net/bbs/viewthread.php?tid=3538342fpage=1 【课件】论文常见问题及成因辨析； http://emuch.net/bbs/viewthread.php?tid=3637978fpage=2 4 ，然后就是关于英语写作和翻译方面的一些心得和建议，帖子如下： 【素材】科技英语翻译和写作； http://emuch.net/bbs/viewthread.php?tid=3568684fpage=1 【教程】中国人英文可以论文最容易犯的 200 个错误； http://emuch.net/bbs/viewthread.php?tid=1094989fpage=2 【素材】英文论文写作 - 很不错的； http://emuch.net/bbs/viewthread.php?tid=1651857fpage=2 【教程】英文文章的写作心得分享； http://emuch.net/bbs/viewthread.php?tid=3420259fpage=2 5 ，最后是一些英语论文写作的惯用句式句型和一个英语写作的润色软件，帖子如下： 【素材】写外文论文的一些惯用句式； http://emuch.net/bbs/viewthread.php?tid=3437640fpage=1 【素材】写英文论文常用句型； http://emuch.net/bbs/viewthread.php?tid=3482914fpage=2 【原创】强烈推荐一款英文润色软件 WhiteSmoke2010 带破解方法； http://emuch.net/bbs/viewthread.php?tid=2290563fpage=2 以上内容仅为个人推荐，想要获取更多更好的科研素材精华资源，请链接到下面的地址： http://emuch.net/bbs/forumdisplay.php?fid=300view=digest 。 来源 3 http://emuch.net/bbs/viewthread.php?tid=1329206fpage=1 小弟不才，迄今才撰写了三篇英文文章，但写作过程中也积累了一点经验，不敢敝帚自珍，今天也斗胆向各位虫友贡献一下。我这几篇文章，不论内容如何，但每次审稿人对于语言的评价都是还不错的， well written ，总结起来不外有三个小窍门： 一是平时多积累。我在日常读文献的时候，如果发现很好的句子句式，都会记录在一个文档里面，如下面的一段话，就是我在一篇文章的摘要中发现的： This paper describes the concept of sensor networks which has been made viable by the convergence of microelectro-mechanical systems technology, wireless communications and digital electronics. First, the sensing tasks and the potential sensor networks applications are explored, and a review of factors influencing the design of sensor networks is provided. Then, the communication architecture for sensor networks is outlined, and the algorithms and protocols developed for each layer in the literature are explored. Open research issues for the realization of sensor networks are also discussed. 文章用词忌重复，中文如此，英文亦然。特别是动词的使用，如在一段话中出现了几个相同的动词，感觉文章就跌价不少，而如果用了几个意思相近而又贴切的词，自然就会增色几分。如上文中的 describe ， explore ， provide ， outline 和 discuss ，就使得文章有了文采，值得学习和收藏。坚持收集例句，素材多了，自然自己的造句的时候就有底子了。此外，还要注意，在收集例句的过程，随着例句的增多，也需要对例句进行整理和分类，方便学习和检索。 二是注意行文中 Transition words 的使用。 Transition words 就是在行文过程中，连接意义相关句子的词，如 Therefore ， thus ， in particular 等等。使用这些词，会使得文章连贯性好，逻辑性强，读起来一气呵成，自然会给审稿人好印象。下面是一个关于 Transition words 的一个总结，供各位虫友参考： Transitions Study Sheet Transitions for time: before, afterward, after, next, then, as soon as, later, until, when, finally, last, meanwhile, during, at times, sometimes, oftentimes Example: WWII broke out in Europe in 1939. During this time the United States remained neutral. It wasn’t until 1941, after Japan bombed Pearl Harbor, that the United States entered the war. After its entry, it was only a matter of time before the Allies defeated Germany and the Axis powers. Transitions for place: in the background, in the distance, beyond, behind, above, below, in front of, elsewhere, in the middle, to the left, to the right Example: My favorite painting is Botticelli’s Birth of Venus. In the middle of the painting stands Venus, the Roman goddess of love, standing on a seashell. She floats majestically above the beautiful water below her. To her left a figure representing wind blows fierce clouds of wind in her direction. To her right a figure behind her attempts to cover her with a blanket and protect her. It is a truly breath-taking piece of art. Transitions for examples: for example, for instance, as an example, like, specifically, consider as an illustration, that is, such as, similar, similarly Example: Oftentimes people who study from history fail to learn from the mistakes of the past. For example, during WWII Hitler decided to invade Russia just before wintertime. This decision was the same decision Napoleon made over a hundred years earlier, and Hitler’s army met a similar fate. Had he learned from his history, Hitler might have avoided making this costly mistake and the outcome for the war might have been different. For instance, if Hitler had decided to invade England by sea rather than Russia by land, he might well have won the war. Transitions for emphasis: chiefly, equally, indeed, even more important, in particular, most important, without a doubt, indubitably, unquestionably, definitely Example: Without a doubt, Chinese food is one of my favorite cuisines. Although I find Japanese and Thai food equally delicious at times, Chinese food is definitely my favorite Asian cuisine. In particular I enjoy the spicy Szechuan style of cooking commonly found in Chinese food. Transitions for restatement: in short, that is, in effect, in other words Example: When I asked my girlfriend to marry me she said, in effect, that she wouldn’t be ready for marriage until after she completed her PhD program. At first I was crushed, that is, I felt like she said no because she didn’t love me anymore. However, after she explained her reasons to me I felt better and agreed with her. In other words, I came away feeling better than I had anticipated. Transitions for comparison: similarly, likewise, also, the same as, different than, opposite, unlike, instead Example: When my older brother was deciding where to go to college he spoke to my father about where he should go. Not surprisingly he went to the same school my father did, MIT. When it was time for me to choose a college I did the exact opposite. I didn’t ask my father where I should go, and as a result, I didn’t also go to MIT like he and my brother did. Instead I went to UCLA. Transitions for concession: although, of course, admittedly, true, doubtless, granted that, no doubt, indubitably, without a doubt, definitely, certainly Example: Some people might be surprised to learn that the two most successful NBA teams of all-time are the Boston Celtics and the Los Angeles Lakers. Although neither of these teams is very good right now, they are the two teams with the most champions in NBA history. The Celtics definitely had the best streak of these two teams; winning eight championships in a row at one point. Admittedly there is always the chance that some future team could break this record, but this seems unlikely. Of course no one can predict the future with any certainty. Transitions for consequence: thus, so, then, it follows, as a result, therefore, hence, consequently, accordingly, because Example: I’m sorry, but I can’t let you turn in your homework late because it wouldn’t be fair to the other students. As a result your grade has dropped lower and you are now failing the class. Consequently you need to get 100% on the final so you can pass the class and then graduate from CAS. Therefore, I suggest you study very hard so I don’t have to fail you. Good luck! Transitions for conclusion: to sum up, in summary, finally, therefore, thus, in conclusion, to conclude Example: Finally, Beijing has a lot of nice places to shop that appeal to tourists. To sum up then, Beijing is a wonderful place to visit because it has beautiful parks and historical monuments, friendly people and lots of nice places to shop. Thus any travelers who are planning to come to China should definitely visit Beijing during their stay. Transitions for addition: furthermore, in addition, besides, next, first, second, moreover Example: UCLA is a wonderful university to attend as an undergraduate. First, it is respected academically and is well-known for its high standards of education. Furthermore, UCLA has a strong network of alumni who often recruit students to come work for them. Moreover students who do such work as undergraduates often receive jobs with these same companies once they graduate. In addition to these two benefits, UCLA also has exciting sports teams that are fun to watch. Besides, with so many good reasons to go to UCLA, why would you want to go anywhere else? 我的第三条经验就是句酷网站， www.jukuu.com ，一个专门找例句的网站，也许有些虫友也知道。我们写文章的时候，很自然会想到一些中文的表达方法，但是常常苦于找不到贴切的英文表达，查电子词典，往往凑出来的句子也是面目全非。句酷网站提供了一个很好的查找例句的渠道（不是广告奥，呵呵），你可以通过中英文关键字，找到很多例句。比如，我想说 “ 值得指出的是 ” ，在句酷里面查了一下，找到了如下几个句子： It is worth emphasizing that... it is worth pointing out that ... A point worth emphasizing is that... 感觉都还不错，都可以选用。更为关键的是，这些例句一般都会有出处，这样就可以根据例句内容和出处来选择比较地道的表述了。我的一个经验是，对于来自 cnki.net 的例句就得小心点，这些都是国内兄弟写的文章中的句子，常常不是很合适。 今天起得早，又睡不着，写这点东西，希望能对大家有一点点启发。上个月自己的第一篇 trans 的 minor revision 刚刚投出去，这些天一直在焦急的等待中，写点东西与大家分享，也顺便给自己祈祈福。第一次在小木虫写帖子，希望大家能喜欢，欢迎大家一起讨论，批评指正，谢谢！
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