Incorrect and incomplete genome annotations poison every experiment that uses them.If an annotation is correct, then these experiments should succeed however, if an annotation is incorrect then the experiments that are based on that annotation are bound to fail. And while most researchers probably don't give annotations a lot of thought, they use them everyday.Įvery time we use techniques such as RNAi, PCR, gene expression arrays, targeted gene knockout, or ChIP we are basing our experiments on the information derived from a digitally stored genome annotation. The first question that occurs to most of us when a genome is sequenced is, "where are the genes?" To identify the genes we need to annotate the genome. Genome sequence itself is not very useful. Genome project from sequencing to experimental application of annotations There are many more projects that use MAKER around the world. Rhagoletis pomonella - apple maggot fly (H Robertson, Univ.Cephus cinctus - wheat stem sawfly (H Robertson, Univ.Zea mays - maize re-annotation (C Lawrence, MaizeGDP).Oryza sativa - rice re-annotation (R Buell, MSU).Diabrotica virgifera - corn rootworm beetle (H Robertson, Univ.parasitic nematode genomes (M Mitreva, Washington Univ).Lactuca sativa - Lettuce (RW Michelmore) - Annotation in progress.Cronartium quercuum - rust fungus (JM Davis, Univ.Arabidopsis thale cress re-annotation (E Huala, TAIR) - Manuscript in preparation.Nannochloropsis - micro algae (SH Shiu, Michigan State Univ.) PubMed.Latimeria menadoensis - african coelacanth () - PubMed.Megachile routundata alfalfa leafcutter bee () - Manuscript in preparation.Columba livia - pigeon (M Shapiro, Univ.Cardiocondyla obscurior - tramp ant (J Gadau, Arizona State Univ.) - Manuscript in preparation.Fusarium circinatum - pine pitch canker (B Wingfield, Univ.Petromyzon marinus - Sea lamprey (W Li, Michigan State) PubMed.Conus bullatus - cone snail (B Olivera Univ.Pogonomyrmex barbatus - red harvester Ant (J Gadau, Arizona State Univ.) PubMed.Linepithema humile - Argentine ant (CD Smith, San Francisco State Univ.) PubMed.Atta cephalotes - leaf-cutter ant (C Currie, Univ.Pinus taeda - Loblolly pine (A Stambolia-Kovach, Univ.Pythium ultimum oomycete (R Buell, Michigan State Univ.) PubMed.Schmidtea mediterranea - planaria (A Alvarado, Stowers Institute) PubMed.MAKER has been used in many genome annotation projects (these are just a few): MAKER can be used for de novo annotation of newly sequenced genomes, for updating existing annotations to reflect new evidence, or just to combine annotations, evidence, and quality control statistics for use with other GMOD programs like GBrowse, JBrowse, Chado, and Apollo. However, MAKER is also designed to be scalable and is thus appropriate for projects of any size including use by large sequence centers. MAKER is an easy-to-use genome annotation pipeline designed for small research groups with little bioinformatics experience. 11.4 Improving Annotation Quality with MAKER's AED score.11.2 Training ab initio Gene Predictors.11.1.8 External Application Behavior Options.11.1.2 Re-annotation Using MAKER Derived GFF3.11 Advanced MAKER Configuration, Re-annotation Options, and Improving Annotation Quality.8.6 Selecting and Revising the Final Gene Model.8.5 Integrating Evidence to Synthesize Annotations.8 Details of What is Going on Inside of MAKER.4.2 Tutorials for custom repeat library generation.4.1 Performance on large computing clusters.3.4 Comparison of Algorithm Performance on Model vs.3.2 What sets MAKER apart from other tools ( ab initio gene predictors etc.)?.2.3 Effect of NextGen Sequencing on the Annotation Process.
love file created specifically to show what I'm trying to do it's not the actual code I'm using for my game. I know I could have each individual function I want to call from the file in question be it's own separate file, and call the function as a chunk, but I'd rather not have 1,000 lua files with just one function each, because most of the functions are quite small and are only called once or twice in the entire game.Īnybody have any idea what's going on, or did I do a really poor job explaining the situation? love file which does pretty much exactly the same thing I did the other night, but for some reason it gives me an error that says the function doesn't exist. Now, include() doesn't work in LOVE, but the other night I tried doing exactly that with loadfile() instead and it worked perfectly, I was able to call a function from that file to set defined in 'a', but I don't have the original code I used.