Ebbie v3.0.9

Ebbie: automated analysis and storage of small RNA cloning data using a dynamic web server.

Motivation

Sequencing projects, such as cloning of small RNAs, result in thousands of sequencing files. Here we describe an automated analysis pipeline, which excises the cloned RNA; uses BlastN to search it against various databases and allows standardized annotation using cgi-scripts. After annotating the new clone, the sequence and its annotation are stored in a MySQL database as well as in a flat file for subsequent BlastN searches. This sequence analysis pipeline eliminates manual mistakes, allows the discovery of multiply cloned sequences and reliably stores sequences and their annotations.

For complete description of Ebbie, please see the accompanying publication in BMC Bioinformatics link here once accepted.

Availability

Ebbiev.3.0.9: all files all perl scripts are available under GNU GPL. For release notes: Release Diary.

Installation on this server

Primarily, these perl scripts are intended to be installed on a local Linux server running apache. It is also feasible to install Ebbie on Mac OSX taken that all modules are available (Ebbie requires perl-mCGI, perl-mDBI and mysql).

Access to local installation.