Influenza Research Database/Virus Pathogen Resource Hands-on Workshop

Location: Erasmus MC, Room COO-5 Rotterdam

Date and Time: May 29, 2017 9:00 - 15:45

Instructors

RichardScheuermannand Yun Zhang, J. Craig Venter Institute, La Jolla, CA, USA

About the Workshop

The Influenza Research Database (IRD, and Virus Pathogen Resource (ViPR; freely available, US NIH/NIAIDsponsored one-stop database and analysisresources to search, analyze, visualize, save and share data aboutmajor human viral pathogens including influenza virus, Arenaviridae, Bunyaviridae, Caliciviridae, Coronaviridae, Filoviridae, Flaviviridae,Hepeviridae, Herpesviridae,Paramyxoviridae, Picornaviridae, Poxviridae,Reoviridae, Rhabdoviridae, Togaviridae, and others. IRD and ViPRcapture various types of information, including sequencerecords, gene and protein annotations, 3D protein structures, immune epitope information, clinicaland surveillance data, host factor data, and novel data derived from comparative genomicsanalysis. Analytical and visualization tools for metadata-driven statistical sequence analysis,multiple sequence alignment, phylogenetic tree construction in super-computing environments, BLAST comparison, short peptide identification, sequencevariation determination, genome sequence annotation, genotype prediction and recombination detection, PCR primer design, Sequence Feature and Phenotypic Variant Type annotation, Influenza virus HA subtype numbering conversion, Influenza virus HA clade classification, Influenza virus surveillance data visualization,protein structure visualization, and host factor data enrichment analysis are also provided. The workshop will include a live demonstration of IRD and ViPRfollowed by hands-onexercises.

Who Should Apply

This workshop is intended to be a full day intensive introduction to the IRD and ViPR Bioinformatics Resource Center. The ideal candidate would have a need to become an expert user of the resource(s).

Computer Access

You will need to have a computerfor hands-on exercises.

Registration

Registration is free, but seating is limited. Please register early to ensure a seat.To do so, fill in the following form in

Location: EMC COO-5

For maps and travel directions, check:

For questions, please email

Hands-on Workshop Agenda(Subject to change)

Erasmus MC, Room COO-5 May 29, 2017

9:00 – 9:30 am / Overview of IRD and ViPR
9:30 – 10:45 am / Section A. Sequence search
  • Influenza virus
  • Search for sequences using metadata-based search interface, view sequence annotations, and subscribe to new sequence email alerts
  • Search for swine H1 sequences by clade classification
  • BLAST for similar sequences
  • Identify short peptides and immune epitopes in proteins
  • View pre-computed consensus sequences
  • Search for and compare animal surveillance records
  • Flavivirus
  • Search for Zika virus sequences and view mature peptide annotations
  • Herpesvirus
  • Search for Human Herpesvirus 1 sequences and view genome annotations

10:45 – 11:00 am / Break
11:00 – 12:00 pm / Section B. Comparative genomics analysis of influenza H7N9 viruses
  • Search for H7N9 HA outbreak sequences
  • BLAST for sequences similar to H7N9 outbreak sequences
  • Save sequences into working sets
  • Construct a phylogenetic tree
  • Run Metadata-driven Comparative Analysis Tool (Meta-CATS)
  • Visualize multiple sequence alignment

12:00 – 1:00 pm / Lunch
1:00 – 1:20 pm / Section B. Comparative genomics analysis of influenza H7N9 viruses (cont’d)
  • Determine if significant positions are located in Sequence Features
  • Highlight significant positions and Sequence Features on protein structure

1:20 – 1:55 pm / Section C. Identification of Serotype-specific Positions in DENV NS1
  • Search for sequences and save sequences into working sets
  • Run Metadata-driven Comparative Analysis Tool (Meta-CATS)
  • Visualize protein sequence alignment
  • Search immune epitope locations

1:55 – 2:25 pm / Section D. Sequence Feature Variant Type analysis
  • Search and analyze an immune epitope Sequence Feature

2:25 – 2:40 pm / Break
2:40 – 3:00 pm / Section E. Sequence annotation
  • Influenza virus HA clade classification
  • Influenza virus HA numbering conversion
  • Influenza virus Sequence Feature annotation
  • Genotype determination and recombination detection
  • Genome Annotator

3:00 – 3:30 pm / Section F. Host factor data analysis
  • Search for host factor experiments and compare biosets and patterns
  • Compare host responses to MERS-CoV and SARS-CoV infections

3:30 – 3:45 pm / Discussions and exit survey