Table of Contents
Genome Sequences
Abundance and complexity of mRNA
Example of mRNA from chick oviduct,
Normalized cDNA libraries
ESTs from normalized cDNA libraries
cDNA clones and ESTs
Genome sequences available
Genome sequencing after mapping
Shotgun sequencing of whole genomes
Shotgun sequencing and assembly
Directed sequencing of BAC contigs
Identifying genes in genomic DNA sequences
Computational tools for predicting genes and important sequences
Genome size
Gene size and number
Compared to worm and fly, human has shorter exons and longer introns on the extremes of the distribution
As G+C increases, gene density increases and introns get shorter
Genome size increases exponentially, but not number of genes
Databases for genomic analysis
Genetic map around MYOD1, 11p15.4
Human Genome Browser view
Ensembl view
Programs for sequence analysis
Results of BLAST search, INS vs. nr
Large scale genome organization
E. coli genome with sequence features
New insights for E. coli
Human chromosomes sequenced
Segmental duplications are common
Comparative Genomics
Paralogous genes
Core proteomes vary little in size
Little change in core proteome size in eukaryotes
Core proteomes are conserved
Types of information one can get
Functional categories in eukaryotic proteomes
Distribution of the homologues of the predicted human proteins
Conserved segments in the human and mouse genome
Expression profiling using microarrays
PSU’s microarray spotting robot
Find clusters of co-regulated genes
OTC problems 1.46-1.49 illustrate use the Web resources from genome sequencing
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Author: Ross Hardison
Email: rch8@psu.edu
Home Page: http://www.bmb.psu.edu/courses/bmb400/default.htm
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