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galaxy-genome-annotation / docker-galaxy-genome-annotation

:whale: Galaxy Docker Image with Tools for Genome Annotation
MIT License
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Wrap NCBI tool kit (includes gnomon gene prediction) #19

Open Eduardo-Alves opened 7 years ago

Eduardo-Alves commented 7 years ago

NCBI pipeline for eukaryotic annotation uses gnomon: "Protein, transcript and RNA-Seq read alignments are passed to Gnomon for gene prediction. Gnomon first chains together non-conflicting alignments into putative models. In a second step, Gnomon extends predictions missing a start or a stop codon or internal exon(s) using an HMM-based algorithm. Gnomon additionally creates pure ab initio predictions where open reading frames of sufficient length but with no supporting alignment are detected." https://www.ncbi.nlm.nih.gov/genome/annotation_euk/process/

There are no license restrictions and the code is part of ncbi toolkit: "NCBI C++ Toolkit provides free, portable, public domain libraries with no restrictions use" https://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/ https://www.ncbi.nlm.nih.gov/viewvc/v1/trunk/c%2B%2B/src/algo/gnomon/

pvanheus commented 7 years ago

More on the use of Gnomon here. Broadly it looks like the Compart tool is used to convert BLAST hits into regions to examine and Splign / ProSplign are used in a manner similar to exonerate to refine alignments. There is much to wrap besides these tools, but as a start, these tools are part of the NCBI C++ toolkit. Compiling the entire toolkit is a large job. The build system would have to be used to only build the necessary components.

Sunny973 commented 6 years ago

I have installed the whole NCBI C++ toolkit on my Linux System, but I cannot find 'gnonom' in the bin directory. And I found no tutorial about Gnomon on the NCBI website... I also tried to contact NCBI, but no response. Anyone knows how to use Gnomon? Thanks!

Biomedinformatics commented 4 years ago

I was trying the NCBI Eukaryotic genome annotation pipeline but was unable to find any maual or tutorial for Gnomon. Can anyone guide me how to use it.

Thanks