BioCloneDB: A database application to manage DNA sequence and gene expression data

Eli Reuveni, Dena Leshkowitz, Oded Yarden*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

2 Scopus citations


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 ( blast/db/). Availability: BioCloneDB is available for academic use along with documentation, screenshots, database scheme and readme files at Contact: Oded Yarden ( il).

Original languageAmerican English
Pages (from-to)277-280
Number of pages4
JournalApplied Bioinformatics
Issue number4
StatePublished - 2005

Bibliographical note

Funding Information:
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).


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