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NOTICE
TIGRscan has now been replaced by a new gene finder called

which is available from www.genezilla.org.  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.

Downloads

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

File
  
Description



tigrscan.tar.gz
Complete source code



tigrscan-arabidopsis.tar.gz

Model files for Arabidopsis thaliana



tigrscan-tetrahymena.tar.gz

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



tigrscan-plasmodium.tar.gz

Model files for Plasmodium falciparum



tigrscan-toxoplama.tar.gz

Model files for Toxoplasma gondii



tigrscan-aspergillus.tar.gz

Model files for Aspergillus fumigatus




Contact: Bill Majoros (bmajoros@tigr.org)