# UGENE - Lab Talk 24.05.21 <!-- Put the link to this slide here so people can follow --> slides: https://hackmd.io/r8cdrbkxR0uYP5tPqdUsAg All rights are reserved to the UGENE company and the video creators. --- Basics of UGENE use for alignments, SNPs, chromatograms, etc. --- ## Download and instal from: - This page: http://ugene.net/download.html - It will detect the system you use: Linux/Windows (if not check for correct format of installation) - It is free and easy. :cat:  --- ## UGENE: http://ugene.net/key_features.html  - Creating, editing, and annotating nucleic acid and protein sequences - Multiple sequence alignment: ClustalW, ClustalO, MUSCLE, Kalign, MAFFT, T-Coffee - Integrated Primer3 package for PCR primer design - Contigs assembly with CAP3 - ... --- ### What will you find in this document? --- 1. How to generate sequence based on chromatogram (.ab1). 2. Easy alignment. 3. Primers design. 4. Phylogenetic trees. 5. Restriction enzymes. 6. Dealing with annotations. 7. Read bam-bai files. 8. Using Workflow Designer (Ready to use NGS workflow). 9. Youtube - UGENE channels recommendations and links. 10. Official webpage - https://doc.ugene.net/wiki/display/QSG/Quick+Start+Guide {%youtube nWS4zIICIAs %} --- --- # :bulb: How to generate sequence based on chromatogram (.ab1) --- - Drag&drop the file or press the Ctrl-O shortcut to open and loud. - Right-click on the chromatogram view and select the Edit new sequence item in the appeared context menu. - The sequence being edited is displayed right above the original one. Two and More Chromatograms: - Drag the required sequence object from the Project. - Lock scales and Adjust scales global actions for the chromatograms. :::success Official webpage links: - Chromatogram Viewer https://doc.ugene.net/wiki/display/UM38/Chromatogram+Viewer - Viewing Two Chromatograms Simultaneously https://doc.ugene.net/wiki/display/UM38/Viewing+Two+Chromatograms+Simultaneously ::: :::info Youtube: - Generate sequence base on the chromatogram- https://www.youtube.com/watch?v=9a1wvynLWBo - The Sanger Reads Editor in UGENE 1.27: https://www.youtube.com/watch?v=lDovNM1oZEw - Rus. - https://www.youtube.com/watch?v=SRKLxf5Nq4o ::: {%youtube lDovNM1oZEw %} --- # :bulb: Easy alignment --- - Drag the required sequence.  - Export (.aln and stats.)  :::success Official webpage links: - Exporting Sequences as Alignment https://doc.ugene.net/wiki/display/UM38/Exporting+Sequences+as+Alignment - Alignment Overview https://doc.ugene.net/wiki/display/UM38/Alignment+Overview - Working with Alignment https://doc.ugene.net/wiki/display/UM38/Working+with+Alignment ::: :::info Youtube: - Making a multiple sequence alignment from FASTA file https://www.youtube.com/watch?v=2pZszPGKnT8 ::: --- # :bulb: Primers design --- - Insert fasta:  - Go to primer3:  - Add sequence to look for and/or parameters:  - Specify the results name:  - Check the positions:  :::success Official webpage links: - Primer3 https://doc.ugene.net/wiki/display/UM38/Primer3 - Primer Algorithm Element https://doc.ugene.net/wiki/display/UM37/Primer+Algorithm+Element ::: :::info Youtube: - Primer Design in UGENE https://www.youtube.com/watch?v=CmQFO_E6xvY&t=17s ::: --- # :bulb: Phylogenetic trees --- - One button to rule them all   :::success Official webpage links: - Building Phylogenetic Tree https://doc.ugene.net/wiki/display/UM38/Building+Phylogenetic+Tree ::: :::info Youtube: - Basic example using UGENE to build a phylogenetic tree https://www.youtube.com/watch?v=fY_jWHq3oG0 - Phylogenetic trees algorithms https://www.youtube.com/watch?v=Ad-HCdo5flo ::: --- # :bulb: Restriction enzymes --- :::success Official webpage links: - Restriction Analysis https://doc.ugene.net/wiki/display/UM38/Restriction+Analysis ::: :::info Youtube: - Searching restriction enzymes cut sites with UGENE https://www.youtube.com/watch?v=sl-_3IcPHTI ::: --- # :bulb: Annotations --- :::success Official webpage links: - Creating Annotation https://doc.ugene.net/wiki/display/UM37/Creating+Annotation ::: :::info Youtube: - Working with a sequence: basic operations https://www.youtube.com/watch?v=R09CIWyDSQk - Working with annotations, part 1: creating annotations https://www.youtube.com/watch?v=vUinIZsWPJI ::: --- # :bulb: Read bam-bai files --- :::success Official webpage links: ::: :::info Youtube: - Browsing BAM files with UGENE Assembly Browser https://www.youtube.com/watch?v=UvIaiF6I6-A ::: --- # :bulb: Workflow Designer --- - Create your own workflow for repetitive tasks or use existing  :::success Official webpage links: - Workflow Samples https://doc.ugene.net/wiki/display/UM38/Workflow+Samples ::: :::info Youtube: - Using Workflow Designer to export sequences from PDB files to FASTA files- https://www.youtube.com/watch?v=s5zp8DZxNVI - Ready to use NGS workflow - https://www.youtube.com/watch?v=nWS4zIICIAs ::: More links: :::spoiler https://www.youtube.com/watch?v=dr4uSMxH3Ok Working with chromatogram- https://www.youtube.com/watch?v=RYz_IhCZwxk Generate sequence base on the chromatogram- https://www.youtube.com/watch?v=9a1wvynLWBo Unipro UGENE podcast #52: The Sanger Reads Editor in UGENE 1.27 https://www.youtube.com/watch?v=lDovNM1oZEw Rus - https://www.youtube.com/watch?v=SRKLxf5Nq4o Dealing with annotations - https://www.youtube.com/watch?v=R09CIWyDSQk https://www.youtube.com/watch?v=vUinIZsWPJI Easy alignment - https://www.youtube.com/watch?v=RYz_IhCZwxk Restriction enzymes- https://www.youtube.com/watch?v=sl-_3IcPHTI Read bam-bai files- https://www.youtube.com/watch?v=UvIaiF6I6-A Primers design- https://www.youtube.com/watch?v=CmQFO_E6xvY&t=17s Unipro UGENE podcast #10: Using Workflow Designer to export sequences from PDB files to FASTA files- https://www.youtube.com/watch?v=s5zp8DZxNVI Ready to use NGS workflow - https://www.youtube.com/watch?v=nWS4zIICIAs UGENE chanel - https://www.youtube.com/watch?v=CmQFO_E6xvY&list=PLSDH2UStQkuaCe3cQrq5RIIJhkK-pkyOc Phylogenetic tree - https://www.youtube.com/watch?v=fY_jWHq3oG0 ::: --- # :100: :muscle: :tada: --- ### Wrap up - Read the manual in the official webpage. - Tak time to push and try icons - you can not mess it up. - Look in youtube and forums online - all is there. - There is a whole community for UGENE users all over the world. Good luck and enjoy this tool! --- ### Thank you! :sheep: You can find me on - Whatsapp - or email me (ksenia.juravel#mail,huji,ac,il) for any question. --- # :fork_and_knife: ---