<it>Ebbie</it>: automated analysis and storage of small RNA cloning data using a dynamic web server

• Main Authors: Unrau Peter J, Wiese Kay C, Ebhardt H Alexander
• Format: Article
• Language: English
• Published: BMC 2006-04-01
• Series: BMC Bioinformatics
• Online Access: http://www.biomedcentral.com/1471-2105/7/185

<p>Abstract</p> <p>Background</p> <p>DNA sequencing is used ubiquitously: from deciphering genomes<abbrgrp><abbr bid="B1">1</abbr></abbrgrp> to determining the primary sequence of small RNAs (smRNAs) <abbrgrp><abbr bid="B2">2</abbr><abbr bid="B3">3</abbr><abbr bid="B4">4</abbr><abbr bid="B5">5</abbr></abbrgrp>. The cloning of smRNAs is currently the most conventional method to determine the actual sequence of these important regulators of gene expression. Typical smRNA cloning projects involve the sequencing of hundreds to thousands of smRNA clones that are delimited at their 5' and 3' ends by fixed sequence regions. These primers result from the biochemical protocol used to isolate and convert the smRNA into clonable PCR products. Recently we completed a smRNA cloning project involving tobacco plants, where analysis was required for ~700 smRNA sequences<abbrgrp><abbr bid="B6">6</abbr></abbrgrp>. Finding no easily accessible research tool to enter and analyze smRNA sequences we developed <it>Ebbie </it>to assist us with our study.</p> <p>Results</p> <p><it>Ebbie </it>is a semi-automated smRNA cloning data processing algorithm, which initially searches for any substring within a DNA sequencing text file, which is flanked by two constant strings. The substring, also termed smRNA or insert, is stored in a MySQL and BlastN database. These inserts are then compared using BlastN to locally installed databases allowing the rapid comparison of the insert to both the growing smRNA database and to other static sequence databases. Our laboratory used <it>Ebbie </it>to analyze scores of DNA sequencing data originating from an smRNA cloning project<abbrgrp><abbr bid="B6">6</abbr></abbrgrp>. Through its built-in instant analysis of all inserts using BlastN, we were able to quickly identify 33 groups of smRNAs from ~700 database entries. This clustering allowed the easy identification of novel and highly expressed clusters of smRNAs. <it>Ebbie </it>is available under GNU GPL and currently implemented on <url>http://bioinformatics.org/ebbie/</url></p> <p>Conclusion</p> <p><it>Ebbie </it>was designed for medium sized smRNA cloning projects with about 1,000 database entries <abbrgrp><abbr bid="B6">6</abbr><abbr bid="B7">7</abbr><abbr bid="B8">8</abbr></abbrgrp>.<it>Ebbie </it>can be used for any type of sequence analysis where two constant primer regions flank a sequence of interest. The reliable storage of inserts, and their annotation in a MySQL database, BlastN<abbrgrp><abbr bid="B9">9</abbr></abbrgrp> comparison of new inserts to dynamic and static databases make it a powerful new tool in any laboratory using DNA sequencing. <it>Ebbie </it>also prevents manual mistakes during the excision process and speeds up annotation and data-entry. Once the server is installed locally, its access can be restricted to protect sensitive new DNA sequencing data. <it>Ebbie </it>was primarily designed for smRNA cloning projects, but can be applied to a variety of RNA and DNA cloning projects<abbrgrp><abbr bid="B2">2</abbr><abbr bid="B3">3</abbr><abbr bid="B10">10</abbr><abbr bid="B11">11</abbr></abbrgrp>.</p>