blocks|key|2755365|text|http://gmod.org/不那么简单--最简单的安装应该为您提供一个blast表单&一个“序列浏览器”界面。还不知道有没有更多的表格.|type|unstyled|depth|inlineStyleRanges|entityRanges|offset|length|data|2755366|(规模相当大-从简单的sqlite到真正的数据库)|2755367|或者，您可能希望查看银河服务器。http://main.g2.bx.psu.edu/|2755368|它的第一个目的是使复杂的基因组查询对于非计算性的人来说很容易，但我不知道它是否有突破。|2755369|干杯，扬尼克|2755370|更新-部分受这篇文章的启发，我们正在开发一个+简单本地blast服务器+作为易于部署的+可供选择的。正在+http://www.sequenceserver.com工作。演示服务器允许您使用稻瘟蚁基因组.+|style|BOLD|2755371|entityMap|0|LINK|mutability|MUTABLE|url|http://gmod.org/|1|http://main.g2.bx.psu.edu/|2|http://www.sequenceserver.com/|3|4|5|http://www.antgenomes.org/^0|0|G|0|0|0|G|Q|1|0|0|0|0|M|10|7|1D|3|2A|K|N|C|2|18|5|3|1H|T|4|2N|6|5|0^^$0|@$1|2|3|4|5|6|7|15|8|@]|9|@$A|16|B|17|1|18]]|C|$]]|$1|D|3|E|5|6|7|19|8|@]|9|@]|C|$]]|$1|F|3|G|5|6|7|1A|8|@]|9|@$A|1B|B|1C|1|1D]]|C|$]]|$1|H|3|I|5|6|7|1E|8|@]|9|@]|C|$]]|$1|J|3|K|5|6|7|1F|8|@]|9|@]|C|$]]|$1|L|3|M|5|6|7|1G|8|@$A|1H|B|1I|N|O]|$A|1J|B|1K|N|O]|$A|1L|B|1M|N|O]|$A|1N|B|1O|N|O]]|9|@$A|1P|B|1Q|1|1R]|$A|1S|B|1T|1|1U]|$A|1V|B|1W|1|1X]|$A|1Y|B|1Z|1|20]]|C|$]]|$1|P|3|-4|5|6|7|21|8|@]|9|@]|C|$]]]|Q|$R|$5|S|T|U|C|$V|W]]|X|$5|S|T|U|C|$V|Y]]|Z|$5|S|T|U|C|$V|10]]|11|$5|S|T|U|C|$V|10]]|12|$5|S|T|U|C|$V|10]]|13|$5|S|T|U|C|$V|14]]]]

something a little less barebones is <a href="http://gmod.org/" rel="nofollow noreferrer">http://gmod.org/</a> - the simplest installation should give you a blast form &amp; a "sequence browser" interface.
Don't know if theres a hmmer form yet... 

(scales pretty well - from a simple sqlite to a real database)

Alternatively, you may want to look into the galaxy server. <a href="http://main.g2.bx.psu.edu/" rel="nofollow noreferrer">http://main.g2.bx.psu.edu/</a> 
It's first aim is making complex genomic queries easy for non-computational people but I dont know if it has a blast out of the box

cheers,
yannick

<hr>

UPDATE - Inspired in part by this post, we are developing a <a href="http://www.sequenceserver.com" rel="nofollow noreferrer">simple local blast server</a> as an easy-to-deploy <a href="http://www.sequenceserver.com" rel="nofollow noreferrer">alternative to wwwblast</a>. Work in progress at <a href="http://www.sequenceserver.com" rel="nofollow noreferrer">http://www.sequenceserver.com</a>. A demo server lets you <a href="http://www.antgenomes.org" rel="nofollow noreferrer">BLAST ant genomes</a>.

blocks|key|1146234|text|这可能有点过分但是..。ncbi有很多可用的软件。链接。|type|unstyled|depth|inlineStyleRanges|entityRanges|offset|length|data|1146235|特别是这。|1146236|entityMap|0|LINK|mutability|MUTABLE|url|http://www.ncbi.nlm.nih.gov/guide/howto/dwn-software/|1|http://www.ncbi.nlm.nih.gov/projects/gbench/^0|P|2|0|0|3|1|1|0^^$0|@$1|2|3|4|5|6|7|P|8|@]|9|@$A|Q|B|R|1|S]]|C|$]]|$1|D|3|E|5|6|7|T|8|@]|9|@$A|U|B|V|1|W]]|C|$]]|$1|F|3|-4|5|6|7|X|8|@]|9|@]|C|$]]]|G|$H|$5|I|J|K|C|$L|M]]|N|$5|I|J|K|C|$L|O]]]]

This will be overkill probably but.... ncbi has a lot of software available. <a href="http://www.ncbi.nlm.nih.gov/guide/howto/dwn-software/" rel="nofollow noreferrer">Link</a>.

In particular, <a href="http://www.ncbi.nlm.nih.gov/projects/gbench/" rel="nofollow noreferrer">this</a>.

blocks|key|1232999|text|还有一个简单的CGI前端与NCBI爆炸包一起分发。您可以从他们的FTP站点下载它，该站点如下：|type|unstyled|depth|inlineStyleRanges|entityRanges|data|1233000|ftp://ftp.ncbi.nih.gov/|offset|length|1233001|entityMap|0|LINK|mutability|MUTABLE|url^0|0|0|N|0|0^^$0|@$1|2|3|4|5|6|7|M|8|@]|9|@]|A|$]]|$1|B|3|C|5|6|7|N|8|@]|9|@$D|O|E|P|1|Q]]|A|$]]|$1|F|3|-4|5|6|7|R|8|@]|9|@]|A|$]]]|G|$H|$5|I|J|K|A|$L|C]]]]

There's a simple CGI front-end distributed with the NCBI BLAST package as well. You can download it from their FTP site, which is here:

<a href="ftp://ftp.ncbi.nih.gov/" rel="nofollow noreferrer">ftp://ftp.ncbi.nih.gov/</a>

blocks|key|1232669|text|这不是你所说的任何一种语言，但有BioPERL，它是专门为DNA和RNA以及其他酸碱和蛋白质基“编程”而设计的功能的集合。|type|unstyled|depth|inlineStyleRanges|entityRanges|data|1232670|在CPAN.org中寻找它|1232671|entityMap^0|0|0^^$0|@$1|2|3|4|5|6|7|F|8|@]|9|@]|A|$]]|$1|B|3|C|5|6|7|G|8|@]|9|@]|A|$]]|$1|D|3|-4|5|6|7|H|8|@]|9|@]|A|$]]]|E|$]]

It's not either of the language you are talking about, but there is BioPERL, which is a collection of functions specifically made for DNA and RNA and other acid and protein base 'programming'

Look for it in CPAN.org

blocks|key|1232761|text|我强烈建议联系生物信息学团体。最重要的是设计数据库并确定其用途。你在标题中提到了DNA，在文本中提到了rRNA+--这些都是完全不同的东西。如果这只是一个错误，没关系--但如果你不理解其中的区别，那就和社区里的人谈谈。|type|unstyled|depth|inlineStyleRanges|entityRanges|data|1232762|由于我参与了这个社区，如果需要的话，您可能希望与MyExperiment社区(http://en.wikipedia.org/wiki/MyExperiment)联系，并提到我的名字。你会找到很多友好的人和帮助。|offset|length|1232763|UPDATE我刚刚注意到你来自曼彻斯特，那里是MyExperiment的中心，所以它确实是一个显而易见的起点！|style|BOLD|1232764|entityMap|0|LINK|mutability|MUTABLE|url|http://en.wikipedia.org/wiki/MyExperiment^0|0|13|15|0|0|0|6|0^^$0|@$1|2|3|4|5|6|7|R|8|@]|9|@]|A|$]]|$1|B|3|C|5|6|7|S|8|@]|9|@$D|T|E|U|1|V]]|A|$]]|$1|F|3|G|5|6|7|W|8|@$D|X|E|Y|H|I]]|9|@]|A|$]]|$1|J|3|-4|5|6|7|Z|8|@]|9|@]|A|$]]]|K|$L|$5|M|N|O|A|$P|Q]]]]

I'd strongly suggest contacting the bioinformatics community. The most important thing is to design the database and decide its purpose. You mention DNA in the title but rRNA in the text - these are completely different things. If it's only a typo, fine - but if you don't understand the difference then talk with people in the community.

Since I'm involved in the community you might like to contact the MyExperiment community (<a href="http://en.wikipedia.org/wiki/MyExperiment" rel="nofollow noreferrer">http://en.wikipedia.org/wiki/MyExperiment</a>) and mention my name if you need to. You'll find lots of friendly people and help.

UPDATE I've just noticed you are from Manchester and that's the hub of MyExperiment so it really is the obvious place to start!

blocks|key|1146284|text|关于GMOD:相对来说，我确信GMOD对于您的应用程序是完全过分的。GMOD不是一个服务器，它是一个工具集合，数据库模式(+Chado+)就是其中之一，而Chado并不是真正适合那些主要拥有序列和ids的人。BioMart也不是一个服务器，它是一个允许模型数据库去标准化的工具，能够足够快地运行全基因组查询。其中一个BioMart客户机(MartView)是作为一个web接口提供的。你现在肯定不想使用Biomart，但我可以通过电子邮件详细解释。我的印象是，你更需要一个基于网络的爆炸客户端才能首先开始。|type|unstyled|depth|inlineStyleRanges|entityRanges|data|1146285|entityMap^0|0^^$0|@$1|2|3|4|5|6|7|D|8|@]|9|@]|A|$]]|$1|B|3|-4|5|6|7|E|8|@]|9|@]|A|$]]]|C|$]]

Concerning GMOD: I am relatively sure that GMOD is complete overkill for your application. GMOD is not a server, it's a collection of tools, the database schema (CHADO) being one of them, and Chado is not really for someone who mostly will have sequences and ids. BioMart is not a server either, it's a tool that permits de-normalization of model databases, to be able to run whole-genome queries fast enough. One of the BioMart clients (MartView) comes as a web interface. You definitely don't want to use Biomart at the moment but I can explain that in detail by email.
I have the impression that you rather need a web-based BLAST client to get started first.

blocks|key|1232981|text|Galaxy:+Galaxy不是一个数据库，它是一个可以使用各种基因组序列(主要是DNA)的工具的网站。Galaxy与UCSC基因组浏览器序列、工具和文件格式紧密相连。所以，如果你想要建立一个全新序列的数据库，那么星系就不适合你了。它也不包括任何爆炸服务器。如果您想要创建一个序列数据库，CHADO作为GMOD的一部分就很接近了，但是我宁愿开始使用文本文件来开始，请参阅上面的帖子。|type|unstyled|depth|inlineStyleRanges|entityRanges|data|1232982|entityMap^0|0^^$0|@$1|2|3|4|5|6|7|D|8|@]|9|@]|A|$]]|$1|B|3|-4|5|6|7|E|8|@]|9|@]|A|$]]]|C|$]]

Galaxy: Galaxy is not a database, it's a website with tools to work with (mostly DNA) sequences from various genomes. Galaxy is tightly linked with the UCSC genome browser sequences, tools and fileformats. So if you want to create a database of entirely new sequences, galaxy is not for you. It doesn't include any BLAST servers either. If you want to create a database of sequences, CHADO as part of GMOD comes close, but I'd rather start use a text file to get started, see my post above.

blocks|key|2755562|text|也许你可以看看Plone4Bio。|type|unstyled|depth|inlineStyleRanges|entityRanges|offset|length|data|2755563|Plone是一个用python编写的扩展的内容管理引擎，它具有很多特性和易于使用的应用程序，因此您可以通过使用论坛、新闻产品等模块来创建您的网站。(我知道你已经知道了，但这只是给出一点背景)。|2755564|Plone4Bio旨在为生物信息学提供一些应用程序.我不知道这个项目有多高级，我还没有使用它，但看起来至少你有一个序列对象和一些可视化的应用程序，可能还有一些应用程序来搜索它们。(p.s.他们在uniprot上使用它--看看任何膜蛋白的“第三方数据”部分)|2755565|我不知道其他的CMS应用程序都是针对生物信息学的，但是也许你也可以很容易地用django实现一些东西，而不需要花费太多的精力。|2755566|entityMap|0|LINK|mutability|MUTABLE|url|http://p4bdemo.biodec.com/|1^0|7|9|0|0|0|0|9|1|0|0^^$0|@$1|2|3|4|5|6|7|S|8|@]|9|@$A|T|B|U|1|V]]|C|$]]|$1|D|3|E|5|6|7|W|8|@]|9|@]|C|$]]|$1|F|3|G|5|6|7|X|8|@]|9|@$A|Y|B|Z|1|10]]|C|$]]|$1|H|3|I|5|6|7|11|8|@]|9|@]|C|$]]|$1|J|3|-4|5|6|7|12|8|@]|9|@]|C|$]]]|K|$L|$5|M|N|O|C|$P|Q]]|R|$5|M|N|O|C|$P|Q]]]]

Maybe you can look at <a href="http://p4bdemo.biodec.com/" rel="nofollow noreferrer">Plone4Bio</a>.

Plone is an extended content management engine written in python, with a lot of features and easy to use applications, so you can create your website by using a collection of modules like forums, products for news, etc... (I know you know this already but it is just to give a bit of background).

<a href="http://p4bdemo.biodec.com/" rel="nofollow noreferrer">Plone4Bio</a> is aimed at providing some plone applications for bioinformatics... I don't know how much the project is advanced and I haven't used it yet, but it seems that at least you have a sequence object and some apps for visualizing it, and probably some applications to search them. (p.s. they use it at uniprot - look at the 'Third party data' section for any membrane protein)

I don't know of any other CMS apps aimed at bioinformatics, but maybe you can also easily implement something with django without too much effort.

blocks|key|1145370|text|不知道信息将以何种格式存储，也不知道如何显示DNA序列(这仅仅是一个长字符串吗？)，您可以只需将每个DNA序列插入MySQL数据库，然后执行以下简单的查询：|type|unstyled|depth|inlineStyleRanges|entityRanges|data|1145371|SELECT+*+FROM+`dna_table`+WHERE+`sequence`+=+$sequence;|code-block|syntax|javascript|1145372|确保使用转义字符串或参数化查询(以防止SQL注入)，但除此之外，这听起来像一个非常简单的DB程序，不应该超过100行代码。|1145373|entityMap^0|0|0|0^^$0|@$1|2|3|4|5|6|7|K|8|@]|9|@]|A|$]]|$1|B|3|C|5|D|7|L|8|@]|9|@]|A|$E|F]]|$1|G|3|H|5|6|7|M|8|@]|9|@]|A|$]]|$1|I|3|-4|5|6|7|N|8|@]|9|@]|A|$]]]|J|$]]

Having no idea about what format the information will be stored in, or how DNA sequences are displayed (is it just a long string?), you may be able to get away with simply inserting each DNA sequence into a MySQL database and then executing a simple query like:

<pre><code>SELECT * FROM `dna_table` WHERE `sequence` = $sequence;
</code></pre>

Make sure you use an escape string or a parameterized query (to prevent SQL injection), but other than that, this sounds like a REALLY simple DB program that shouldn't be more than about 100 lines of code.

blocks|key|2755407|text|我同意:你应该把你的问题发到bbb@bioinformatics.org或bioperl邮件列表上。|type|unstyled|depth|inlineStyleRanges|entityRanges|data|2755408|“容易创建带有网站搜索表格的通用序列数据库”的问题似乎过于笼统。序列数据库是(id，sequence)的列表，它本身不需要任何工具支持。至少我看不出有什么理由你需要一个工具来解决这个问题。|2755409|我想你的问题是:是否有一个可以在本地安装的作为webform的BLAST客户端？有一些:计划也许值得一试，虽然我从来没有让它运行。BioPerl有用于独立爆炸执行(http://doc.bioperl.org/releases/bioperl-1.0/Bio/Tools/Run/StandAloneBlast.html)的对象，并且可以以图形方式显示结果。Debian/Ubuntu拥有ncbi-+tools+-bin和ncbi数据，这些数据可以在几秒钟内安装必要的工具和数据库。|offset|length|2755410|与其考虑工具支持，我更愿意一起破解一个10行CGI脚本，该脚本使用输入序列在您拥有的Fasta文件上执行blast，然后查看用户是否已经对此感到满意。|2755411|关注编程语言:如果您愿意，可以使用shell脚本(*)来完成这一任务。你花的时间可能比堆叠溢出上的帖子还少.;-)|2755412|(*)对疑神疑鬼的计算机科学的同事们的注意:它将是生物学家的内部应用程序，他们不知道操作系统和操作符重载之间的区别，所以sql注入非常不可能.|2755413|我认为这是一个例子，在这个例子中，过早的优化已经够邪恶的了，因为您可以在设计一个过于复杂的系统时花费大量的时间来完成一项简单的任务。本着敏捷编程的精神，如果您喜欢软件工程的流行词，您可以简单地将一些东西组合在一起，然后在您的用户上进行尝试，然后再考虑体系结构。|2755414|entityMap|0|LINK|mutability|MUTABLE|url|http://doc.bioperl.org/releases/bioperl-1.0/Bio/Tools/Run/StandAloneBlast.html^0|0|0|2A|26|0|0|0|0|0|0^^$0|@$1|2|3|4|5|6|7|X|8|@]|9|@]|A|$]]|$1|B|3|C|5|6|7|Y|8|@]|9|@]|A|$]]|$1|D|3|E|5|6|7|Z|8|@]|9|@$F|10|G|11|1|12]]|A|$]]|$1|H|3|I|5|6|7|13|8|@]|9|@]|A|$]]|$1|J|3|K|5|6|7|14|8|@]|9|@]|A|$]]|$1|L|3|M|5|6|7|15|8|@]|9|@]|A|$]]|$1|N|3|O|5|6|7|16|8|@]|9|@]|A|$]]|$1|P|3|-4|5|6|7|17|8|@]|9|@]|A|$]]]|Q|$R|$5|S|T|U|A|$V|W]]]]

I agree: You should post your question to bbb@bioinformatics.org or the bioperl mailing list.

The question "easy creation of a generic sequence database with a website search form" seems too general. A sequence database is a list of (id, sequence) and by itself doesn't need any tool support. At least I don't see any reason why you would need a tool for that.

I think your question is: Is there a BLAST client as webform that one can install locally? There are some: PLAN might worth a try though I never had it running. BioPerl has objects for standalone BLAST execution (<a href="http://doc.bioperl.org/releases/bioperl-1.0/Bio/Tools/Run/StandAloneBlast.html" rel="nofollow noreferrer">http://doc.bioperl.org/releases/bioperl-1.0/Bio/Tools/Run/StandAloneBlast.html</a>) and can display the results graphically. Debian/Ubuntu Med have ncbi-tools-bin and ncbi-rrna-data which install the necessary tools and databases in a couple of seconds.

Instead of pondering tool support I would rather hack together a 10 line CGI script that executes blast with an input sequence onto the Fasta files that you have and then see if the users aren't already happy with that. 

Concerned about the programming language: If you like, you can do this with a shell script (*). That might even take you less time than the posting on stackoverflow... ;-) 

(*) Note to paranoid computer science collegues: it's going to be an internal application for biologists who don't know the difference between an operating system and operator overloading, so sql injections are very very unlikely...

I think this is an example where premature optimization is evil enough, in the sense that you can loose tons of time with designing a system too complex for a simple task. In the spirit of agile programming, if you like software engineering buzzwords, you might simply hack something together and then try it on your users before thinking about the architecture.

I'd like to create an rRNA sequence database with a web front end for the lab I work in. It seems common in biology to want to search a large number of sequences using alignment algorithms such as BLAST and HMMER, so I wondered if there is any existing php/python/rails projects that allow easy creation of a generic sequence database with a website search form?

UPDATE: <a href="http://gmod.org/wiki/Main_Page" rel="nofollow noreferrer">GMOD</a> is the type of server I was looking for. I was also suggested to look at <a href="http://www.biomart.org/index.html" rel="nofollow noreferrer">BioMart</a> too which looks to have a similar functionality.

Are there any existing solutions for creating a generic DNA sequence database with a website front end?

翻译质量差，导致语言生硬或混乱。

没有提供实际的解决方法或示例。

解答不清晰，无法理解或解决问题。

页面排版不美观，阅读体验差。

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我想为我工作的实验室创建一个带有web前端的rRNA序列数据库。在生物学上，想要使用BLAST和HMMER等对齐算法搜索大量序列似乎很常见，所以我想知道是否有任何现有的php/python/rails项目允许使用网站搜索表单轻松创建通用序列数据库？UPDATE：是我正在寻找的服务器类型。我也被建议看，它看起来具有类似的功能。

问是否有任何现有的解决方案来创建一个带有网站前端的通用DNA序列数据库？
EN

回答 10

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问是否有任何现有的解决方案来创建一个带有网站前端的通用DNA序列数据库？EN

回答 10

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问是否有任何现有的解决方案来创建一个带有网站前端的通用DNA序列数据库？
EN