yun zhang j. craig venter institute june 23, 2014
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Sequence Variation Identification and Functional/Structural Inference in the Influenza Research Database (IRD) and Virus Pathogen Resource ( ViPR ) . Yun Zhang J. Craig Venter Institute June 23, 2014. Challenges for Sequence Analysis. Sequence Variation Identification - PowerPoint PPT PresentationTRANSCRIPT
Sequence Variation Identification and Functional/Structural Inference in the Influenza Research Database (IRD) and Virus Pathogen Resource (ViPR)
Sequence Variation Identification and Functional/Structural Inference in the Influenza Research Database (IRD) and Virus Pathogen Resource (ViPR) Yun ZhangJ. Craig Venter InstituteJune 23, 2014Challenges for Sequence AnalysisSequence Variation Identification
Functional/Structural Inference
Influenza virus A_NS1_nuclear-export-signal_137(11)Sequence Feature (SF) Curated from literature, public archives, direct submission2,747 influenza SFs, 543 Dengue SFs, 301 HCV SFs, 296 Vaccinia SFs
Clin Infect Dis. (2013) 57 (4): 622-624Manual analysisData amountSubjectiveNovel analysis toolStatisticalGenotype-phenotype correlation
http://www.library.ucsf.edu/node/2337
Buried in literature2
www.fludb.org
www.viprbrc.orgSequence Variation Analysis Workflow
Influenza A_ H3_ experimentally- determined-epitope_156(7)
4Use Case: Influenza H7N9 Virus2013 Influenza virus A H7N9 outbreakH7 viruses have historically circulated in birds and horsesH7N9 human cases: 1st human case reported in March 2013, 410 human cases as of April 2014, fatality rate 22%
Sequence variations involved in human adaptation?5Sequence Search H7N9 HA & Similar Sequences
2. HA sequences highly similar to a typical H7N9 human strain1. H7N9 HA complete sequences 6Meta-CATS Analysis Grouping
similar older H7 sequences H7N9 human HA sequences
H7N9 outbreak HA sequences vs. similar older H7 sequences 7Meta-CATS Analysis Results
Verify Results on Alignment
Older H7 avian strainsH7N9 human strains235L/I9Meta-CATS Analysis Results
Variant Position Mapped to Sequence Features161211Variant Positions Visualized on Protein StructureVariant position 235Ligands4BSC: H7N9 HA in Complex with 6'-SLN
Human H7N9 Influenza Virus Haemagglutinin (with Asn-133 Glycosylation) in Complex with Human Receptor Analogue 6'-SLN12SummaryA novel sequence variation identification and functional/structural inference workflow
www.viprbrc.org
www.fludb.orgFree you from the time-consuming process 13Acknowledgments NIAIDHHSN272200900041CJ. Craig Venter InstituteRichard Scheuermann (PI)Brian Aevermann, M.S.Douglas Greer, Ph.D.Brett Pickett, Ph.D.Rick Stanton, M.S.E.ELucy Stewart, MBAYun Zhang, M.Sc.
VecnaChris Larsen, Ph.D.Al Ramsey, Ph.D.Guangyu Sun, Ph.D.
LANLCatherine Macken, Ph.D.Mira Dimitrijevic
Southern Methodist UnivMonnie McGee, Ph.D.Mengya Liu, Ph.D.Northrop GrummanScott Stuart, Program ManagerEd Klem, Ph.D., Project ManagerZhiping Gu, Ph.D.Sherry HeWenjie HuaWei JenSanjeev KumarXiaomei Li, Ph.D.Jason LucasBruce QuesenberryBarbara RotchfordTom Smith, Ph.D.Hongbo Su, Ph.D.Bryan WaltersSam Zaremba, Ph.D.Hongtao Zhao, Ph.D.Liwei Zhou, Ph.D.
NIAID / DMIDAlison Yao, Ph.D., Contracting Officer Representative, Microbial Genomics & Advanced Technologies
Andrei Gabrielian, Ph.D., Office of Cyber Infrastructure and Computational Biology
Diane Post, Ph.D., CEIRS Project Officer14