Sequence and structure databanks

Sequence and structure databanks can be divided into many different categories. One of the most important is

Supervised databanks with gatekeeper. Examples:

SwissprotRefseq (at NCBI)

Entries are checked for accuracy.+ more reliable annotations-- frequently out of date

Repositories without gatekeeper. Examples:

GenBankEMBLTrEMBL

Everything is accepted + everything is available-- many duplicates-- poor reliability of annotations

Description of Group B Streptococcus Pan-genome

Genome comparisons of 8 closely related GBS strains

Tettelin, Fraser et al., PNAS 2005 Sep 27;102(39)

Method

Bacterial CoreGenes that are shared among all

Bacteria

Bit score cutoff 50.0 (~10E-4)

f(x) = A1*exp(-K1*x) + A2*exp(-K2*x) + A3*exp(-K3*x) + Plateau

Genes without homologs

f(x) = A1*exp(-K1*x) + A2*exp(-K2*x) + A3*exp(-K3*x) + A4*exp(-K4*x)

+ A5*exp(-K5*x) + Plateau

Decomposed function

Core

Essential genes(Replication, energy,

homeostasis)

~ 116 genefamilies

Extended Core

Set of genes that define groups or species

(Symbiosis,photosynthesis)

~ 17,060 genefamilies

Accessory PoolGenes that can be used to distinguish strains or

serotypes(Mostly genes of unknown functions)

~ 114,800 geneFamilies uncovered so far

76.6%

3.8%

19.6%

Gene frequency in individual genomes

Core

Extended Core

Accessory Pool

f(x) = A1*exp(-k1*x) + A2*exp(-k2*x) + A3*exp(-k3*x) + A4*exp(-k4*x) + A5*exp(-k5*x) + Plateau

1/k1 = 0.48 1/k2 = 2.31/k3 = 10.161/k4 = 31.401/k5 = 162.6

A1 = 939.4A2 = 731.1A3 = 455.2A4 = 328.6A5 = 385.5

Number of genomes added

Kézdy-Swinbourne Plot

0

50

100

150

200

250

300

350

400

450

500

-100 0 100 200 300 400 500 600

delta x = 10

2030405060708090100110120130

Novel genes after looking in x genomes

Nov

el g

enes

aft

er lo

oki

ng

in x

+ ∆

x ge

nom

es

~230 novel genes per genome

A Kézdy-Swinbourne Plot plot can be used to estimate the value that a decay function approaches as time goes to infinity.

Assume the simple decay function f(x) = K + A e-kx , then f(x + ∆x) = K + A e-k(x+∆x).Through elimination of A: f(x+∆x)=e-k ∆x f(x) + K’

For the plot of f(x+∆x) against f(x) the slope is e-k ∆x. For x both f(x) and f(x+∆x) approach the same constant : f(x)K, f(x+∆x)K. (see the def. for the decay function)The Kézdy-Swinbourne Plot is rather insensitive to deviations from a simple single component decay function.

More at Hiromi K: Kinetics of Fast Enzyme Reactions. New York: Halsted Press (Wiley); 1979

Kézdy-Swinbourne Plot

0

50

100

150

200

250

300

350

400

450

500

-100 0 100 200 300 400 500 600

delta x = 10

2030405060708090100110120130

Novel genes after looking in x genomes

Nov

el g

enes

aft

er lo

oki

ng

in x

+ ∆

x ge

nom

es

~230 novel genes per genome