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About TigrScan

TigrScan is a new 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.
Some accuracy results: click here.

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)