#Add annotations snapgene how to
#Add annotations snapgene download

Tblastx=/work/GIF/software/programs/ncbi-blast/2.2.28+/bin/tblastx #location of NCBI+ tblastx executableįormatdb= #location of NCBI formatdb executableīlastall= #location of NCBI blastall executable Makeblastdb=/work/GIF/software/programs/rmblast/2.2.28/bin/makeblastdb #location of NCBI+ makeblastdb executableīlastn=/work/GIF/software/programs/ncbi-blast/2.2.28+/bin/blastn #location of NCBI+ blastn executableīlastx=/work/GIF/software/programs/rmblast/2.2.28/bin/blastx #location of NCBI+ blastx executable #-Location of Executables Used by MAKER/EVALUATOR To ensure proper parsing of the files, make sure that there are no spaces between the equal sign and the path to the files. I will only use blastn, blastx, tblastx, repeatmasker, exonerate, snap, gmhmme3(GeneMark), and augustus. Maker_opts.ctl - This is the key control file that will be subject to change for each round of maker. Maker_bopts.ctl - This one controls the parameters of each program if you want to change the default settings. Maker_exe.ctl- This file points to the executable programs that we will be using. #Of course you can use maker to copy these files for you #Copy the 3 maker control files, which are essentially config files needed to run makerįor f in /work/GIF/remkv6/Purcell/Abalone/29_MakerP/02_MakerRun2/maker_* do cp $f. This includes the predicted transcripts and proteins from all genome assemblies in this clade.

#Add annotations snapgene download

Download all transcriptional resources for the clade in which your species residesįor the soybean cyst nematode, that includes all publicly available resources for the Tylenchida. This leads us to the first step of finding all transcriptional and protein resources for the initial MAKER prediction. While there are multiple ways to run Maker, all tips and tutorials that I have run across have always done the maker annotation first, and then incorporated the other ab-initio predictors subsequently. Is there a specific order to run different predictors in Maker? Here is a Maker tutorial that gave me the idea to use BUSCO to train Augustus. There are a number of nice Maker tutorials that can found online. The “Genome Annotation and Curation Using MAKER and MAKER-P” publication has a list of example protocols that may be helpful and may add some detail to my choices below. This version of maker includes the addition of multiple gene ab-initio prediction tools as well as AED score support for gene models. This is the original publication for the MAKER2 gene prediction pipeline. This is the original MAKER publication, which details more about the general MAKER algorithm, when MAKER lacked all other gene predictors besides SNAP.

#Add annotations snapgene how to

I have outlined how to perform a gene annotation of the soybean cyst nematode ( Heterodera glycines) genome using Maker2. Tutorial of how to run Maker2 gene annotation pipeline