Co-op in the Upton Lab

Transcript

1. Viral Bioinformatics in the Upton lab Chris Kelly
2. What is the VBRC?   Viral Bioinformatics Resource Centre (VBRC)   VBRC maintains the domain virology.ca, which   Provides resources for the use of other laboratories   Maintains a database of viral sequences + annotations   Provides access to open source sequence analysis tools
3. What do the people do?   Two types of people work in the lab (in general):   Programmers   Create and maintain tools (Mostly Java, utilizing Java Web Start distribution)   Systems administration – primarily website maintenance.   Odd technical jobs   Biologists   Annotations / sequence analysis   Maintenance of quality data
4. My work term   My background: Biochemistry   My primary interest: Computation   Hired to interface between biologists and programmers
5. My work term   Majority of time: Suffix Tree Searcher (STS) paper   Write paper on program.   The theory turned out to be fairly complex.   I didn’t yet know what I was talking about   Before writing, I had to conduct research on suffix trees   Theory   Implementation   Applications.   Testing of STS   Performance   Feature validation
6. My work term   Everything else   Website maintenance   Writing STS documentation   Sequence annotation   Odd research jobs   Odd technical jobs
7. Suffix Trees (Brief)   Index a character string such that substring of length n can be found in n or less computational steps.   Significance   Search time does NOT depend on size of data set!   Given a suffix tree of the Oxford English Dictionary (~350 million characters).   We can determine whether or not the word “dogs” is present in 4 or less steps   Search time is independent of dictionary size
9. Suffix Trees   Extended further, we can use suffix trees to find   Number of occurrences of pattern in each genome   Location of pattern in genome   Which input genomes contain the pattern
10. Suffix Tree Searcher (STS)   STS is a program written in the Upton lab.   Distributed with java web start (JWS)   Provides:   Automatic updates   No setup required   Written in C (backend) and Java (GUI).   Constructs suffix trees and input sequences   Uses the trees to analyze the sequences.   Rapid pattern searching   Exploration of common patterns between sequences
11. Suffix Tree Searcher (STS)
12. Influenza A Neg8   Influenza A is a –sense ssRNA virus.   Chris identified a long conserved ORF on the genomic (- sense) strand.   167 codons in older viruses   Extended to 216 codons in newer viruses   216 codon ORF conserved only in human-derived viruses.   Perhaps provides selective advantage in human hosts   Searched for this in different influenza A viruses   In many non-human viruses, 3 or less nucleotide substitutions required to extend ORF to 216 codons   This research is ongoing…
13. Odd jobs   NGS sequence read assembly, annotation   Other annotations   Literature review
14. Maintenance   Website maintenance   Technical documentation for STS   Odd technical jobs
15. The end