MetaGene is no longer available

As of December 15th 2009, the MetaGene tool is no longer available on the RGD website.  Over the years since the tool was first written, most or all of the online resources that MetaGene used have been either moved or changed sufficiently to render the MetaGene tool unusable.  During a round of testing in October 2009 we found that all of the "request" submissions that we made via this tool failed.  Unfortunately, it took several hours for the tool to determine that the requests had failed making the situation even more problematic.  As such the decision was made to remove the tool completely rather than simply leave it as "available but unsupported".

If you are looking for DNA analysis software, here are some alternatives that you can try:

Web-based Tools
 Center for Biological Sequence Analysis
 Center for Biological Sequence Analysis

Tools for Gene Finding and Locating Splice Sites:
    HMMgene:  Genes in eukaryotes
    NetGene2:  Intron splice sites in human, C. elegans and A. thaliana DNA
    NetStart:  Translation start in vertebrate and A. thaliana DNA
    NetUTR:  Splice sites in 5' UTR regions of human genes
    Promoter:  Transcription start sites in vertebrate DNA
    RNAmmer:  Ribosomal RNA sub units

They also have a suite of tools for protein analysis…

 Promoter Prediction Tool at BGDP
Berkeley Drosophila Genome Project
 M. G. Reese's Promoter Prediction tool is one of a suite of tools hosted by the Berkeley Drosophila Genome Project.  This is the current location of the NNPP tool which MetaGene used.

SoftBerry has an extensive suite of DNA sequence analysis tools.  However, the online version is primarily for demonstration purposes.  Softberry specifies that the tools are only available free of charge to academic users and they only support "light-volume use" (less than 15 executions per day per academic domain).  Please respect this limitation.

 A licensed version of the software is also available for users to run locally.  Please contact the company for more information.


A tutorial for doing Eukaryotic Gene Prediction is located at:

The content is a bit outdated as some of the tools they use are no longer at the locations they state (e.g. the Sanger Institute no longer supports the tools previously located there.  Those tools appear to now be located at  But if you are just starting out with this kind of analysis, this could provide a good starting point.


Downloadable Tools

A suite of software that can be downloaded and run locally is available from the University of Maryland's Center for Bioinformatics & Computational Biology.

 University of Maryland's Center for Bioinformatics & Computational Biology

 The Center provides tools for

All programs are open source.