GenomeThreader Gene Prediction Software

GenomeThreader is a software tool to compute gene structure predictions. The gene structure predictions are calculated using a similarity-based approach where additional cDNA/EST and/or protein sequences are used to predict gene structures via spliced alignments. GenomeThreader was motivated by disabling limitations in GeneSeqer, a popular gene prediction program which is widely used for plant genome annotation.


References have been omitted for brevity; you can find them and more details on the implementation in the GenomeThreader paper. How to take advantage of these features and many more is described in depth in the GenomeThreader manual. Please consult the FAQ page for frequently asked questions. All mentioned files and scripts are also part of the GenomeThreader distribution (see below).


GenomeThreader is available free of charge for non-commercial research institutions. To obtain a copy, please fill out the license agreement and send it to us by fax or email (as described in the document). As soon as we receive your license agreement, we send you a username and password by email which you can use to download GenomeThreader.



The following sites use GenomeThreader. This list is not intended to be comprehensive.

If you want to appear on this list, please drop me a note.


GenomeThreader has been cited in the following publications:

If I missed a publication which cites GenomeThreader, please drop me a note.


GenomeThreader is being actively developed by the following individuals:


Please cite the following article in publications about research using GenomeThreader:

For in-depth information about GenomeThreader please refer to the following dissertation: