Advantages of entire sequence
	-understanding of functions of genes by sequence similarity
	-direct access to DNA by PCR
		"hybridization by computer easier than by DNA"
	-noncoding DNA provides insights into evolution, coding, information management

Genome sequencing- 
    Methodology
	-Automated Dideoxy sequencing with fluorescent dyes
	-combination of dividing into segments, shotgun sequencing, and ordered sequencing to
		fill gaps 

    Sequencing projects
           
                -Example: yeast 
                        -http://genome-www.stanford.edu/Saccharomyces/maps.html
                        -12,136,020 nt (12,057,500 nt without mitochondrial genome) 
                                sequenced
                        -entire length with  969,000 nt of unsequenced repeats= 
                                13,105,020 nt
                        -70% of DNA codes something
                        - 6,111 genes predicted (40% have unknown function)
                        -1 gene every 2 kB
	

            Arabidopsis database project (AtDB)
                main site: http://genome-www3.stanford.edu/atdb_welcome.html    
                
                -sequencing YAC, BAC and P1 libraries of chromosomes
                -fidelity needs to be >97% for useful database
                -sequence scanned for genes: introns, coding regions
                        prediction success of 31% for GENSCAN and 37% for GENEFINDER

                Feb 2000: 112,503 bases sequenced (86.5% of genome)

		Arabidopsis sequence summary-NCBI Site
			Example of complete sequence from Chromosome II- annotated, click on location
				close-up on chromosome II


        Other Plants: http://probe.nalusda.gov:8300/plant/index.html
     AAtDB--Arabidopsis;     Alfagenes--alfalfa (Medicago sativa)
     BeanGenes--Phaseolus and Vigna;   ChlamyDB--Chlamydomonas reinhardtii
     CoolGenes--cool season food legumes;   CottonDB--Gossypium hirsutum
     GrainGenes--wheat, barley, rye and relatives;     MaizeDB--maize;  MilletGenes--pearl millet;     
      PathoGenes--fungal pathogens of small-grain cereals;  RiceGenes--rice;    RoseDB--Rosaceae;   
     SolGenes--Solanaceae; SorghumDB--Sorghum bicolor;   SoyBase--soybeans
     TreeGenes--forest trees;  Mendel--plant-wide gene names

	Cheaper approaches:
		1) End sequence of ordered BAC library- provides some sequence info
		2)ESTs- Expressed sequence tags
         		Random cDNA clones that the end has been sequenced
                        -uses: rapid gene identification
                                mapping 

                        -Arabidopsis Gene Index (AGI)  
				Aug 1999: 38,133 ESTs sequenced. 
                                -18732 single copies produced. 
                              	-example of an EST- similarity to hexokinase


	What you can do with sequence
		A) Go from map position to potential gene through the database
		B) Do computational hybridization to find genes based upon expected sequence
		C) Compare plant species, families, relationships more exactly
		D) Clone and characterize diversity of sequence among individuals

Functional genomics- linking sequence to function
	
	Two types of info useful for function-
		a) what is phenotype of gene mutation?
			-with sequence can selectively mutate gene, e.g. yeast
		b) when and where is the gene expressed?
	
			-EST provides expression information by comparison of EST databases 
				isolated under different conditions
			-Microarrays and DNA chips

Microarrays: array of different cDNA clones - hybridization to fluorescently-labeled cDNA 
	collected under different conditions allows hybridization to show differences accross 
	the array when each is expressed

DNA chips:  Based upon having sequence already (e.g. genomic sequence). Oligonucleotides are 
	synthesized on chips at high density.  Hybridization to labeled cDNA populations 
	indicates which oligos represent expressed mRNAs
	
 
	

Links:
Mapping and Sequencing the Human Genome
Arabidopsis EST
TIGR- Arabidopsis main page
BAC cloning in Arabidopsis
List of Genes found from Sequencing Chromosome V of Arabidopsis
Maize genome database
Listing and links of genes cloned in Snapdragon
Genome analysis Manual- sequence retrieval sources
Gene Finder software for Arabidopsis- Wang, CSHL
Links to Microarrays and DNA chips
     -Animation on DNA chips- AVI or Quicktime- Affymetrix
Image of microarray- and link to description
Arabidopsis Functional Genomics Consortium- Microarrays and gene KOs
List of Gene finding programs-predict transcriptional start sites, intron/exon boundaries

Last revised: March 2000- Straney