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Comprehensive Workflow for the Genome-wide Identification and Expression Meta-analysis of the ATL E3 Ubiquitin Ligase Gene Family in Grapevine

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BioCloneDB: A Database Application to Manage DNA Sequence and Gene Expression Data.

Eli Reuveni¹, Dena Leshkowitz, Oded Yarden

¹Department of Plant Pathology and Microbiology, Faculty of Agricultural, Food and Environmental Quality Sciences, The Hebrew University of Jerusalem, Rehovot, Israel.

Applied Bioinformatics

|November 29, 2005

Summary

BioCloneDB is a user-friendly database for managing DNA clone sequence information in molecular genetics labs. It automates batch sequence annotation, simplifying high-throughput projects and replacing manual BLAST searches.

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An Integrated Approach for Microprotein Identification and Sequence Analysis

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Area of Science:

Molecular Genetics
Bioinformatics

Background:

Managing local repositories of DNA clone sequence information is crucial for molecular genetics laboratories.
High-throughput sequencing and gene expression projects require efficient data management and analysis tools.

Purpose of the Study:

To introduce BioCloneDB, a user-friendly database with a web interface for managing DNA clone sequence information.
To provide a tool that links sequence information with gene expression data for high-throughput projects.
To automate batch sequence annotation using BLAST searches, simplifying analysis for researchers.

Main Methods:

BioCloneDB utilizes a web interface for user interaction.
The system automates batch sequence annotation by performing BLAST searches against user-specified databases.
The software is open-source and installable on Linux or UNIX operating systems.

Main Results:

The application was tested using 1400 expressed sequence tags from Neurospora crassa.
Automated annotation of sequences was successfully performed.
Results showed significant changes attributed to data accumulation in the nr database.

Conclusions:

BioCloneDB offers a streamlined approach to managing sequence information and performing batch annotation.
The tool enhances efficiency in molecular genetics laboratories, particularly for high-throughput studies.
It eliminates the need for manual individual BLAST searches and complex UNIX-based batch processing.