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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.

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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