Before started

We all know that the user guide is too long and nobody want to read it. So I recorded some tutorial videos for users. Please keep in mind, these videos only for demonstration. For details, please refer to the User guide and our paper Lei Li, Siriruk Changrob, Yanbin Fu et al., Librator, a platform for optimized sequence editing, design, and expression of influenza virus proteins. 2021. You'are also welcome to email me or Patrick for more information. Enjoy!

Sorry for the voice volume issue of these videos, I had a cold (not COVID) and didn't have a mic on that day.

Tutorial Videos

Analysis

• Path setting in Librator

  Users can set paths for all required tools and databases.
• Start with a new database

  1) Create a new database in Librator 2) Import sequences into Librator
• Brief introduction of Librator user interface

  Brief introduction of Librator user interface
• HA numbering system and multiple sequence alignment viewer in Librator

  1) Users are allowed to access the H1/H3 numbering of the selected sequence. 2) We also allow users to customize their epitope settings.
• Phylogenetic analysis in Librator

  Users are allowed to generate a phylogenetic tree (Maximum Likelihood tree) for selected sequences. Nucleotide and Amino Acid trees are available.
• Identify mutations in Librator

  Users are allowed to identify mutations between any two sequences. If you have a template sequence and a mutated sequence (e.g. escape mutants) and want to quickly know all the mutated residues, you can use this function to identify all mutations and annotate mutation information on your mutated sequence.
• Generate SeqLogos and visualize peptide conservations a 3D structure

  1) Users can generate sequence logos for multiple selected sequences. 2) Users also can visualize peptide conservations for selected sequences on a 3D structure using PyMOL or UCSF Chimera. The structure annotation code will also be displayed in a pop-up window.

Sequence design

• Mutating sequence in Librator

  Users can generate new sequences with mutations based on any existing sequence.
• Making antigen probes in Librator

  Users are allowed to generate antigen probes for given HA sequences with one click.
• Design chimeric/mosaic protein sequences in Librator

  Users can transplant epitopes/regions from sequences of different subtypes. This function could be helpful for designing chimeric HA protein. Regions being removed from base sequence and that being inserted from donor sequence are not necessary to have the same length.

Gibson cloning

• Generate Standardized Gibson Clone fragments for HA/NA in batches

  Users can generate standardized Gibson Clone Fragments for HA/NA sequences in batches. Those fragments are reusable because they are following the same design.
• Generate Gibson clone sequence for any given sequence

  Besides HA/NA sequences, Librator also allows users to split any of their sequences into fragments. Users can use this function for some novel research subjects, e.g. COVID-19 proteins.