Sanger Sequencing

indel

SNP?

throughput: How many bases per day?

What is the read length?

indel = purposely deleted sections

Single Nucleotide Polymorphism

35,000

1000

454 Sequencing (new)

Base reads?

Reads per run?

Bases per run?

How long does it take?

200-400 base reads

200,000 reads per run

100,000,000 bases per run

1 day

Solexa Sequencing (new)

How many bases per run

How many base reads

Paired-end mode

How much $$$ per run

20,000,000 bases per run

76-100 base reads

Paired-end mode

$4,000 per run

Two Strategies for Human Genome Sequencing

1. Mapped Clones

2. Whole Genome Shotgun

Repeating Sequences

LINEs

SINEs

Retro-Virus-Like Elements

DNA transposon fossils

Transposons

Class 1

Class 2

Transposons: sequences that can move around a genome

(jumping genes)

Class 1: retrotransposons: makes RNA that is inserted into DNA by reverse transcriptaase

Class 2: DNA transposons that are inserted into DNA by transposases

Gene Data (Human)

What percent code for genes?

What percent codes for proteins?

How many genes? Human, Fly, and Worm

4-5% for genes

1-2% for proteins

Human: 20,000

Fly: 13,000

Worm: 18,000

Yeast Genome

# chromosomes

# genes

What % of genome are genes

___ gene every ____ bases

____ ribosomal RNA genes in _______

____ transfer RNAs

___ of gene have introns

16 Chromosomes

6000 Genes

70% of genome is genes

1 gene per 2000 bases

140 ribosomal RNA

(tandem = repeated sections to insure contiguous and continuous transcription)

275 transfer RNA

4% of gene have introns

Telomeres

regions that contain _____

These may be associated with _______

contain Ty5

transposons

Escherichia Coli

Gram Neg/Pos?

# bases

Genes are organized into ______

# of the above?

____ genes, distance?

genes account for ___% of genome

What % involved in regulatory function?

Gram neg

4,600,000

organized into operons

2600 operons

4200 genes, 118 bases per gene

Genes account for 87% of genome

Only 11% is involved in regulatory function