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<p>First generation bioinformatics tools consisted of applications, usually with a text-based interface, which performed a specific task well. The computational biology tool best-known among biologists is probably BLAST, an algorithm for searching large databases of protein or DNA sequences. The NCBI provides a popular web-based implementation that searches their massive sequence databases. Also fairly early on, due to the amassing of sequence and annotation data, keyword search engines which were able to resolve gene and protein synonyms were important. Computer scripting languages such as Perl (thanks to its regular expressions handling facilities) and Python are often used to interface with biological databases and parse output from bioinformatics programs written in languages such as C or C++. Communities of bioinformatics programmers have set up free open source bioinformatics projects to develop and distribute the tools and modules they produce.</p>

<p>As the data sources expanded and diversified, both in content and geography, bioinformatic meta search engines, such as Sequence profiling tools, emerged to help find relevant information from several databases. These meta search engines might index data from a local server or even from a panel of third party services.</p>

<p>More recently, SOAP-based interfaces have been developed for a wide variety of bioinformatics applications allowing an application running on one computer in one part of the world to use algorithms, data and computing resources on servers in other parts of the world. A large availability of these SOAP-based bioinformatics web services, along with the open source bioinformatics collections, lead to the next generation of bioinformatics tools: the integrated bioinformatics platform. These tools range from a collection of standalone tools with a common data format under a single, slick standalone or web-based interface, to integrative and extensible bioinformatics workflow development environments.</p>

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<h3><span class="mw-headline">Related topics</span></h3>

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<ul>

<li>Aluru, Srinivas, ed. <em>Handbook of Computational Molecular Biology</em>. Chapman &amp; Hall/Crc, 2006. <a class="internal" href="http://en.wikipedia.org/w/index.php?title=Special:Booksources&amp;isbn=1584884061"><font color="#0066cc">ISBN 1584884061</font></a> (Chapman &amp; Hall/Crc Computer and Information Science Series) </li>

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<li><a class="external text" title="http://bioinformatics.org/" rel="nofollow" href="http://bioinformatics.org/"><font color="#0066cc">Bioinformatics Organization (Bioinformatics.Org): The Open-Access Institute</font></a> </li>

<li><a class="external text" title="http://www.embnet.org/" rel="nofollow" href="http://www.embnet.org/"><font color="#0066cc">EMBnet</font></a> </li>