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Note to the users: the new release (v1.30) is significantly improved in terms of performance. For large files of assembly contigs, the running time could be reduced from days to a few mins. (Read more about this in the "releases" file included in the package).

FragGeneScan is an application for finding (fragmented) genes in short reads. It can also be applied to predict prokaryotic genes in incomplete assemblies or complete genomes.

FragGeneScan was first released through omics website ( in March 2010, where you can find its old releases. FragGeneScan migrated to SourceForge in October, 2013.

If you use FragGeneScan, please cite:
Mina Rho, Haixu Tang, and Yuzhen Ye. FragGeneScan: Predicting Genes in Short and Error-prone Reads. Nucl. Acids Res., 2010 doi: 10.1093/nar/gkq747

TransGeneScan is a sister program for gene finding in metatranscriptomic sequences (

FragGeneScan Web Site




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Additional Project Details

Intended Audience

Information Technology, Healthcare Industry

User Interface


Programming Language

Perl, C



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