Free gene browser

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smeesm19
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Free gene browser

I thought this new tool might be of interest to some other people on this forum.

There is a free gene browser available from Bio::Neos, called GANT.
It is a standalone application that lets you search for a gene and view the sequence, structure and annotation. The annotation is loaded from public data sources but the application is pluggable so as new plugins are developed for data sources you can just download the new plugin and view the annotation.

There is also a primer picking capability that interfaces to an optimized Primer3 server. It is a nice interface for picking primers, you just click the sequence you want to amplify and select Pick Primers from the menu. It is fast also, you can design primers for a whole gene in less than a minute.

The software is free and can be downloaded from http://gant.bioneos.com

ryan_m
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Thanks for the post. Just

Thanks for the post. Just for my own interest, what sets this apart from another freely available genome browser such as GBrowse?

Ryan

qiang wang
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thanks, downloaded

thanks, downloaded

ryan_m
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The ModelMaker tool available

The ModelMaker tool available through NCBI appears to accomplish much of the same stuff without the need to download or install any tools or data.

Ryan

smeesm19
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Ryan,

Ryan,

Sorry for the delay in responding, the reply emails got buried in my spam folder...

Thanks for the links to the other software, I had not heard of them before. Briefly looking at ModelMaker, I'm not sure from the description that it does the same thing as the GANT software. ModelMaker describes itself as allowing you to create an mRNA from genomic data. GANT allows you to view a gene and associated annotation from public sources. Also it has an interface to primer3 for easy primer design.

It looks like GBrowse and GANT are similar. They both are gene browsers that serve up genomic data and annotation. I think the biggest difference appears to be that GBrowse is a webserver that needs to be downloaded and installed, viewed in a web browser. GANT is a stand alone application, and with that you get a richer and more responsive interface.

Again, thanks for the info, I'll check them out more closely when I get some time.

ryan_m
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Thank you for the added

Thank you for the added information. I'm sure that this software does offer some nice features that set it apart from GBrowse etc, but I am just trying to say that there are free tools that do similar things. As an aside, the UCSC genome browser shows public annotations from many different sources and allows you to add any 'custom annotation' tracks you want. It also has an "in-silico" PCR tool for designing PCR experiments. Although it does not 'design' primers for you (you still need to do that), it will tell you if you can expect any off-target results with your primers.

Ryan