Augustus tutorial | Installation | gene prediction #bioinformatics #tutorial

AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences. It can be run on this web server, on a new web server for larger input files or be downloaded and run locally. It is open source so you can compile it for your computing platform. You can now run AUGUSTUS on the German MediGRID. This enables you to submit larger sequence files and allows to use protein homology information in the prediction. The MediGRID requires an instant easy registration by email for first-time users. Full script in on GitHub https://github.com/gravitiwork/StudyTech_scripts/tree/main/003_Augustus_Scripts 1️⃣ Search "augustus tool" https://bioinf.uni-greifswald.de/augustus/ === Go to "Download augustus" === Go to "You find AUGUSTUS for Download" https://github.com/Gaius-Augustus/Augustus 2️⃣ Install directly by super user sudo apt install augustus augustus-data augustus-doc 3️⃣ After installation, Check the species database model for augustus augustus --species=help 2#&1 | tee species_list === identifier saccharomyces_cerevisiae_S288C 5️⃣ Run the augustus augustus --species=saccharomyces_cerevisiae_S288C Scerevisiae_Trinity.fasta --UTR=off --gff3=on | tee output 6️⃣ Check the output # ----- prediction on sequence number 4 (length = 1452, name = TRINITY_DN275_c0_g2_i1) ----- # # Predicted genes for sequence number 4 on both strands # start gene g5 ####################################### use the unique name "start gene" to get gene on 3 line before ###### Use the grep function echo 'start gene' # start_gene_line echo 'name' # name_line grep -w -B 3 -f start_gene_line output --no-group-separator 2#&1 | tee report_01 grep -w -B 0 -f name_line report_01 --no-group-separator 2#&1 | tee report_id ###### open the data on libra Calc ###### Use text to column to seperate the sequence id ✉️Email- [email protected] Email me for further contact 📢 Save my video URL on a notepad in your lab computer. So that you can get this video 📢 Subscribe to my Study tech youtube channel. Because it is free for you but it will help me a lot. 💻 System configuration Procession- Intel i5 4th gen, 1.7 GHz, 4 CPU(or thread) RAM-8GB Boot and working drive- 256GB SSD OS- Linux Mint 21.1 Cinnamon 📢 Guys, if you need any tutorial or help regarding Bioinformatics work, we will try to help you by Video or Chat. Fill free to ask in the comment section. If you are very new to Bioinformatics and have some very basic and silly questions. You are most welcome. Don't hesitate to ask us. You can write in the comment section. =========== Jump to 🏷️ Video specific tags augustus gene prediction, augustus tutorial, augustus gene prediction tutorial, augustus software, augustus genome annotation, augustus bioinformatics, augustus gene prediction tool, augustus command line, gene prediction, gene prediction tools, genome annotation, ab initio gene prediction, eukaryotic gene prediction, fungal gene prediction, augustus Linux, augustus installation, augustus ubuntu, augustus conda, augustus bioconda, command line bioinformatics, augustus training, train augustus, augustus species model, gene prediction fungi, gene prediction plants, gene prediction eukaryotes, augustus gene prediction, augustus tutorial, augustus gene prediction tutorial, augustus bioinformatics, genome annotation, gene prediction, ab initio gene prediction, augustus linux, augustus installation, bioinformatics tutorial, genome annotation tutorial, gene prediction tools, computational biology, genomics tutorial, augustus command line, augustus fungi, bioinformatics for beginners bioinformatics for beginners, gene prediction explained, genome annotation tutorial, phd bioinformatics, msc bioinformatics, life science bioinformatics, #ncbi #genomics #beginners #tutorial #howto #omics #research #biology #ngs #python ♫♫♫♫♫♫ Music used in video ♫♫♫♫♫♫ mortals-feat-laura-brehm--future-trap--ncs---copyright-free-music Track: Warriyo - Mortals (feat. Laura Brehm) [NCS Release] Music provided by NoCopyrightSounds. Watch: http://NCS.lnk.to/MortalsAT/youtube Free Download / Stream: http://ncs.io/Mortals