Where to download NCBI Gnomon?

Question

[ulike]

Anyone knows where to download NCBI Gnomon? I couldn't find the link anywhere on NCBI. I also tried to contact NCBI, but no response.

Thanks!

Answer 1

[h.mon]

You have to download the NCBI C++ Toolkit, you will find GNOMON under src/algo/gnomon. Be sure to read the online docs very, very carefully, compiling it may prove a challenge - I never came across a more roccoco build system. In particular, the usual "./configure && make && make install" will not work.

I downloaded the toolkit to compile ProSplign, and in the end gave up.

[ulike]

Surprisingly, I can install NCBI C++ toolkit with just ./configure and make, but I haven't validated my installation.

Do you guys know a Gnomon tutorial? I didn't find one in the NCBI C++ toolkit book.

[h.mon]

Cool, nice to know. Did you compile the whole toolkit, or manage to compile just GNOMON?

I do not have a tutorial, if you dig NCBI pages deep enough, I believe you should find - they have truckloads of documentation.

[ulike]

I compiled the whole toolkit.

I didn't find anything related to 'Gnomon' or 'Gene prediction' with search bar on NCBI toolkit page. I'll try looking deeper into it.

Maybe I should stay with MAKER, which does a similar job and is very easy to use.

[sunny_shen312]

Have you fixed the problem? I also could not find a manual on Gnomon...

Answer 2

[Neilfws]

I'm pretty sure it's an in-house tool, not available for download. I see I was wrong :)

The PDF "Gnomon - NCBI eukaryotic gene prediction tool" describes their annotation pipeline in some detail. Note that the Gnomon algorithm is based on Genscan. It does not look like a system that anyone else could easily reproduce ;)