prokaryotic genome annotation template and all needed components
I am new on Ergatis. Our system administrator just installed it for me without any component installed.
Based on Orvis J, et al 2010 Bioinformatics, 36 components are minimum required for bacterial annotation, I am wondering anyone is kindly willing to share with me the automated prokaryotic genome annotation template. I am assuming that all needed components should be listed in the template file.
3.1.1 Bacterial genome annotation
Ergatis includes a pipeline template for automated prokaryotic genome annotation that is composed of 36 analysis components. These include gene structure prediction and evaluation, RNA analysis, homology searches, frameshift analysis and functional prediction. Predicted transcripts are assigned functional names, Enzyme Commission numbers, gene symbols and GO terms where possible. The final output is a BSML file that can be loaded into a Chado database instance. Execution of this pipeline on a Pyrobaculum species, with a genome size of 2.2 megabases, yielded 2863 predicted genes. The pipeline had 202 704 commands overall and ran in 216 CPU hours, or 3.8 actual hours when distributed on our compute grid. Ergatis and this pipeline template are used to support the IGS annotation engine (Giglio).