生物信息学国外教程2010版课件.pptVIP

Eukaryotic Genomes: Fungi Wednesday, November 18, 2009 Genomics 260.605.01 J. Pevsner pevsner@;Many of the images in this powerpoint presentation are from Bioinformatics and Functional Genomics by J Pevsner, copyright ? 2009 by Wiley-Blackwell. These images and materials may not be used without permission. Visit ;Schedule;Outline of today’s lecture;Introduction to fungi: phylogeny;Eukaryotes (Baldauf et al., 2000);Fungi and metazoa are sister groups;Classification of fungi;Classification of fungi;Alternate classification of fungi;Outline of today’s lecture;Introduction to Saccharomyces cerevisiae;Sequencing the S. cerevisiae genome;Features of the S. cerevisiae genome;Features of the S. cerevisiae genome;Page 703;Fig. 17.3 Page 703;ORFs in the S. cerevisiae genome;ORFs in the S. cerevisiae genome;ORFs in the S. cerevisiae genome;http://mips.gsf.de/;Revising the S. cerevisiae gene count through comparative genomics;Comparing the DNA sequences from several species makes it possible to find regulatory regions — short sequences that turn genes on and off — and eliminate spurious gene predictions. Red boxes highlight areas of sequence similarity between at least two species. Functional sequences — genes and regulatory elements — tend to be conserved across all species. The figure shows how one true regulatory element and one correctly identified gene might emerge from a comparison of four yeast species. Salzberg SL (2003) Nature 423:233;Kellis et al. (2003) Nature 423:241. ;The N50 size is the length such that 50% of the assembled genome lies in blocks of the N50 size or longer. (N50 contig length = 26,260 kb for human reference assembly);Predicted ORFs are shown as arrows pointing in the direction of transcription. Orthologous ORFs are connected by dotted lines and are coloured by the type of correspondence: red for 1-to-1 matches, blue for 1-to-2 matches and white for unmatched ORFs. Sequence gaps are indicated by vertical lines at the ends of contigs, with the e