BioCloneDB

A Database Application to Manage DNA Sequence and Gene Expression Data

Abstract

BioCloneDB is a user-friendly database with a web interface to assist molecular genetics laboratories in managing a local repository of sequence information linked to DNA clones. This tool is designed to assist in high-throughput sequence and gene expression projects, providing a link between both types of information. The unique feature of the application is the automation of batch sequence annotation following BLAST® searches, which is supported by easy-to-use web interfaces. Furthermore, any set of sequences can be annotated against any sequence database. This replaces the need to perform and analyse individual web BLAST® searches or the need to learn how to produce batch searches and perform analysis in a UNIX® operating system. BioCloneDB is open-source software that can be installed on Linux or UNIX® operating systems. To test the application, we used 1400 expressed sequence tags obtained from the filamentous fungus Neurospora crassa. The results were analysed and compared with published results and they show a significant change due to the accumulation of the data in the nr database (ftp://ftp.ncbi.nih.gov/blast/db/).

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Acknowledgements

This research was supported by BARD, the US — Israel Binational Agricultural Research and Development fund. DL was supported by Israel Ministry of Science grant no. 1424 to Center of Knowledge for Bioinformatics Infrastructure (COBI).

We thank Dvorah Weisman and Arye Harel for helpful advice and Zahi Paz for assistance in web design.

he authors have no conflicts of interest that are directly relevant to the content of this article.

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Correspondence to Dr Oded Yarden.

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Availability: BioCloneDB is available for academic use along with documentation, Screenshots, database scheme and readme files at http://bioclonedb.agri.huji.ac.il/

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Reuveni, E., Leshkowitz, D. & Yarden, O. BioCloneDB. Appl-Bioinformatics 4, 277–280 (2005). https://doi.org/10.2165/00822942-200504040-00007

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Keywords

  • Neurospora Crassa
  • Structure Query Language
  • Annotation Procedure
  • Annotation Module
  • Common Gateway Interface