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TIGRscan has now been replaced by a new gene finder called

which is available from  All development efforts for TIGRscan have been diverted to the new program, which will remain open-source and freely downloadable from the above URL. Significant enhancements to the program are expected in the very near future.

About TigrScan

TigrScan is a gene finder based on the Generalized Hidden Markov Model framework, similar to Genscan and Genie. It is highly reconfigurable and includes software for retraining. It is written in highly optimized C++. The run time and memory requirements are linear in the sequence length. Graph-theoretic representations of the high scoring open reading frames are provided, allowing for exploration of sub-optimal gene models.

It utilizes Interpolated Markov Models (IMMs).

Execution speed: about 12 Kb/sec on a 3.2 GHz Pentium IV  (<3 days to process Human genome).
Memory requirements: generally under 40 Mb RAM total footprint for a 400Kb sequence.


TigrScan is available for download as OSI Certified Open Source Software under the Artistic License. Pre-trained model files are also available.


Complete source code


Model files for Arabidopsis thaliana


Model files for Tetrahymena thermophilis (trained on Plasmodium falciparum and on long Tetrahymena ORFs)


Model files for Plasmodium falciparum


Model files for Toxoplasma gondii


Model files for Aspergillus fumigatus

Contact: Bill Majoros (