GeneMachine: A Unified Solution for Performing Content-Based, Site-Based, and Comparative Gene Prediction Methods

Please note that this software is no longer being supported or updated.

Izabela Makalowska, Joseph F. Ryan, and Andreas D. Baxevanis

Genome Technology Branch, National Human Genome Research Institute,
National Institutes of Health, Bethesda, Maryland 20892 USA.

A number of free-standing programs have been developed in order to help researchers find potential coding regions and deduce gene structure for long stretches of anonymous DNA. We have developed a gene identification tool called GeneMachine which allows users to query multiple exon and gene prediction programs in an automated fashion. BLAST searches are also performed in order to see whether a previously- characterized coding region corresponds to a region in the query sequence. A suite of Perl programs and modules are used to run MZEF, GENSCAN, GRAIL2, FGENES, RepeatMasker, Sputnik, BLASTX and BLASTN. The results of these runs are then parsed and written into ASN.1 format. The resulting ASN.1 file can then be opened using NCBI Sequin, in essence using Sequin as both a workbench and a graphical viewer. The main feature of GeneMachine is that the process is fully automated; the user is only required to launch GeneMachine and then open the resulting file with Sequin. Annotations can then be made to these results prior to submission to GenBank, thereby increasing the intrinsic value of these data.

GeneMachine, as well as other software developed at NHGRI, can be freely downloaded.

Last Modified: Monday, 17-Oct-2016 08:16:14 EDT