09ViralGenomics(生物信息学国外教程2010版).ppt

* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * Example of genotyping tool from NCBI retrovirus resource reference sequence with the highest score Los Alamos National Laboratory (LANL) databases provide a major HIV resource. See / LANL offers -- an HIV BLAST server -- Synonymous/non-synonymous analysis program -- a multiple alignment program -- a PCA-like tool -- a geography tool Bioinformatic approaches to HIV: LANL Page 586 LANL offers many HIV tools including analysis algorithms Fig. 14.17 Page 588 /Resist_DB/protease_mutation_map.htm On Friday Egbert Hoiczyk will give a lecture on bacteria. Monday we will cover chapter 14 (bacteria and archaea). Then on Wednesday we will have computer lab on bacteria. Check the /chapter14 site to find a word document describing the exercises, as well as web links. After that we move on to the eukaryotes. Next… * * * * * * * * * * * * * * * * * * * * * * * * * * Growth of Influenza Virus Sequences in GenBank 10/10 /genomes/FLU/growth.html Holmes et al. (2005) performed phylogenetic analyses of 156 complete genomes of human H3N2 influenza A viruses collected over time (1999-2004) in one location (New York State). Phylogenetic analysis revealed multiple reassortment events. One clade of H3N2 virus, present since 2002, is the source for the HA gene in all subsequently sampled viruses. Large-scale influenza virus genome analysis Holmes EC, et al. Whole-genome analysis of human influenza A virus reveals multiple persistent lineages and reassortment among recent H3N2 viruses. PLoS Biol. 2005 Sep;3(9):e300. Page 576 Evolutionary Relationships of Concatenated Major Coding Regions of Influenza A Viruses Sampled in New York State during 1999–2004. The maximum likelihood phylogenetic tree is mid-point rooted for purposes of clarity, and all horizontal branch lengths are drawn to scale. Bootstrap values are shown for key nodes. Isolates assigned to clade A (light blue), clade B (yellow), and clade C (red) are indi