Name
Title | ||
|---|---|---|
Ebbie: automated analysis and storage of small RNA cloning data using a dynamic web server. |
Abstract | ||
|---|---|---|
Background: DNA sequencing is used ubiquitously: from deciphering genomes(1) to determining the primary sequence of small RNAs (smRNAs) (2-5). 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(6). Finding no easily accessible research tool to enter and analyze smRNA sequences we developed Ebbie to assist us with our study. Results: Ebbie 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 Ebbie to analyze scores of DNA sequencing data originating from an smRNA cloning project(6). 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. Ebbie is available under GNU GPL and currently implemented on http://bioinformatics.org/ebbie/ |
Year | DOI | Venue |
|---|---|---|
2006 | 10.1186/1471-2105-7-185 | BMC Bioinformatics |
Keywords | Field | DocType |
dna sequence,regulation of gene expression,data processing,algorithms,internet,bioinformatics,microarrays | Genome,Small RNA,Biology,Primer (molecular biology),DNA sequencing,Bioinformatics,Cloning,Genetics,Dynamic web page,DNA microarray | Journal |
Volume | Issue | ISSN |
7 | 1 | 1471-2105 |
Citations | PageRank | References |
0 | 0.34 | 1 |
Authors | ||
3 | ||
Name | Order | Citations | PageRank |
|---|---|---|---|
| H. Alexander Ebhardt | 1 | 7 | 0.95 |
| Kay C. Wiese | 2 | 164 | 19.10 |
| Peter Unrau | 3 | 7 | 0.95 |