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Target audience: postdoctoral researchers 


City: Bogota  or Brussels  or Nijmegen  or Liverpool  or Norwich  or Kuala Lumpur  or Faro 

  • Multiple Sequence Alignment with Jalview and Protein Structure and Function Modelling

    14 - 15 May 2018

    Liverpool, United Kingdom

    Elixir node event
    Multiple Sequence Alignment with Jalview and Protein Structure and Function Modelling Date: Monday 14th to Tuesday 15th May 2018 Time: 9.00 to 17.00 Location: MSTC, Sherrington Building, University of Liverpool, L69 3BX Overview This two day hands-on training course is aimed at students and researchers who want to gain practical understanding of the tools and approaches for protein sequence, structure and function prediction and analysis. In day 1, participants will be introduced to Jalview - a free desktop application for the visualisation and comparative analysis of protein, DNA and RNA sequences. Jalview can integrate data from Ensembl, Uniprot, PDBe, Rfam and Pfam, and can access a range of tools for multiple sequence alignment, conservation analysis and secondary structure and disorder prediction, including the widely used JPred4. On the second day, participants will learn to use Jalview’s 3D structure visualisation capabilities in conjunction with UCSF Chimera, and take a whistle-stop tour of the methodologies and tools for prediction and analysis of Protein 3D structure and function. Participants are encouraged to bring their own protein analysis problems and time will be reserved at the end of day 2 for discussion. Register using the link on the Jalview website: Day 1: Multiple Sequence Alignment and Analysis with Jalview Workshop trainers: Dr Jim Procter and Dr Suzanne Duce 9 9.15 Introduction to the Workshop 9.15 10.30 Session 1.Loading sequences, structures and alignments with Jalview Coffee break 11 12.30 Session 2. Multiple alignment Creation and Alignment Reliability Lunch 1.30 3pm Session 3. Phylogenetic trees and subfamily analysis of Proteins and CDS Coffee break 3.30 5pm Session 4. Protein secondary structure and disorder prediction, and working with annotation Day 2: Protein Structure Analysis and Modelling Workshop trainers: Dr Jim Procter and Dr Dan Rigden 9 9.15 Introduction to Workshop Day 2 9.15 9.30 Introduction to Protein 3D Structure 9.30 10 Viewing and Comparing 3D structures with Jalview and UCSF Chimera 10 10.30 Mapping sequence conservation to Biological Assemblies with Jalview Coffee Break 11 12.30 Functional analysis of Protein Structures Lunch 1.30 2.30 Homology modelling and model quality evaluation 2.30 3.15 Ab initio models and searching for fold matches 3.15 3.30 Wrap up: Function Analysis and 3D models Coffee Break 4pm 5pm Analyse your own protein sequences and structures. 2018-05-14 09:00:00 UTC 2018-05-15 17:00:00 UTC Dr Jim Procter and Dr Dan Rigden MSTC, Sherrington Building, University of Liverpool, Liverpool, United Kingdom MSTC, Sherrington Building, University of Liverpool Liverpool Merseyside United Kingdom L69 3BX University of Liverpool Dr Jim Procter and Dr Suzanne Duce, School of Life Sciences, University of Dundee, Dundee University of Dundee PhD studentspostdoctoral researchersprinciple investigatorsLife Science Researchersbioinformaticians 45 workshops_and_courses registration_of_interest Jalviewmultiple sequence alignmentMSAprotein sequence protein structure protein predictionHomology modellingAb initio modelsChimerasubfamily analysisPhylogenetic treesProtein secondary structureUniversity of DundeeUniversity of Liverpool
  • EMBO Practical Course Tree building: Advanced concepts and practice of phylogenetic analysis

    24 - 29 September 2018

    Faro, Portugal

    EMBO Practical Course Tree building: Advanced concepts and practice of phylogenetic analysis The use of phylogenetic methods to reconstruct the evolutionary history of molecular sequences is a vital part of biological research. These methods underpin studies on the evolution and epidemiology of plant and animal parasites and disease-causing organisms, and more generally they allow an objective analysis of the patterns and processes generating biological diversity. To carry out phylogenetic analysis properly, it is necessary to have a good understanding of the strengths and weaknesses of the key methods and approaches. This EMBO Practical Course has been designed to provide the theoretical and practical skills needed to carry out state-of-the-art phylogenetic analyses. The past few years have seen have an explosion in new methods of analysis including the application of Bayesian analysis methods, the development of improved non-stationary models that better represent the dynamics of sequence evolution, the application of population genetic theory to phylogenies through the use of multispecies coalescent, and the development of methods for high-throughput genome-wide analyses. This EMBO Practical Course has been designed to cater for these newest methods and for understanding how they relate to the more traditional methods. Our goal is to teach technical sophistication without losing sight of the need for a critical attitude to data and analyses. 2018-09-24 09:00:00 UTC 2018-09-29 16:00:00 UTC Cymon J. Cox, CCMAR CCMAR - Center of Marine Sciences, Faro, Portugal CCMAR - Center of Marine Sciences Faro Algarve Portugal 8005-319 Molecular modelling Phylogenetics CCMAR, Centre for Marine Sciences Cymon J. Cox - EMBO CCMAR UALG PhD studentspostdoctoral researchersAcademicsIndustry 20 workshops_and_courses by_invitationregistration_of_interest Phylogenymolecular evolutionmolecular modellingBayesian inferenceMaximum likelihood inferencephylogenomics
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