BIOL 202- Genomics

Genome projects

Research and technology development efforts aimed at mapping and sequencing all of genome

Proteome

the entire set of proteins expressed by a given cell or group of cells

ORF

Looks like gene but is not, computer programs can identify ORFs by cDNA

How can exons be identified

1. cDNA cloning and amplifying in vector

2. cDNA direct sequencing next to DNA

cDNA libraries

Contain smaller fragments of DNA, and only include exons of genes expressed by the sample tissue

Can be used to make vectors that can be amplified

Identifies introns indirectly by comparisons in all exons

Exposed sequence tags (ESTs)

Short cDNA with only one end, can determine boundaries of an exon

BLAST search

comparison of sequence data to all known sequences to confirm predicted genes

Either nucleotide or aa

Match indicates candidate gene is real

Codon bias

nonrandom usage of multiple codons encoding the same amino acid (some used more than others)

This is because there are more tRNAs for that codon

Predicted ORFs should match codon patterns of species if it is real

Predicted gene

Using evidence from BLAST, codon bias, sequence motifs, EST, and cDNA to predict gene sequences

Binding-site-prediction programs can predict gene

How much of genome is shared between us

99.9%

.1% is due to 3M base differences

copy number variation (CNV)

differences among individuals in the number of copies of a region of the genome, accounts for most of sequence variation

Copy number polymorphism is associated with many diseases

Exome

all exons in a genome, small portion of our genome but encodes all genes

Exome sequencing

A strategy of sequencing all exons of human using a DNA exon library

Allows screening of de novo mutations, cancer cells, comparisons to target gene changes

1. Shear DNA into ss

2. Bind to immobilized exon probes

3. Elute and amplify exon hybrids

4. Sequence exons