Linear Error Correcting Codes for Modeling the Ribosome and Proteins - - PowerPoint PPT Presentation

Linear Error Correcting Codes for Modeling the Ribosome and Proteins

Mario Enrique Duarte Gonz´ alez

Advisor: Prof. Reginaldo Palazzo Jr.

State University of Campinas - UNICAMP FEEC - Communications Department

January 19-30, 2015

Mario Enrique Duarte Gonz´ alez 2015 SP Coding and Information School

Analogy: Ribosome and Communication system

Biological system transmits information (DNA and Proteins). Proteins are used for every process inside cells. Goals:

1

Model Ribosome

2

Represent Proteins This model was introduced by: (Rocha, 2010) and (Faria, 2011).

C A U A U C G U A

. . .

mRNA

N={A,C,G,U}

Ribosome | Modulator

“Genetic Code” | “Signal Constellation” Translation

H I D V

. . .

Histidine, Isoleucine, ..., Valine

Protein

A={Amino Acids} #A = 20

Codon 1 Codon 2 Codon np

GC:

NxNxN→A

Source

Channel encoder

Channel

C A U A U C G U A

. . .

mRNA

N={A,C,G,U}

Ribosome | Modulator

“Genetic Code” | “Signal Constellation” Translation

H I D V

. . .

Histidine, Isoleucine, ..., Valine

Protein

A={Amino Acids} #A = 20

Codon 1 Codon 2 Codon np

GC:

NxNxN→A

Source

Channel encoder

Channel

Mario Enrique Duarte Gonz´ alez 2015 SP Coding and Information School

Strategy for Modeling the Ribosome and Proteins

Our Strategy:

1

Design LECC’s that represent nucleotide chains and their translated proteins for deducing information about ribosomes.

2

Relate properties of proteins and concepts of coding theory.

C A U A U C G U A

. . .

mRNA

N={A,C,G,U}

Ribosome | Modulator

“Genetic Code” | “Signal Constellation”

H I D V

. . .

Histidine, Isoleucine, ..., Valine

Protein

A={Amino Acids} #A = 20

Codon 1 Codon 2 Codon np

Source

Channel encoder

Channel

C A U A U C G U A

. . .

mRNA

N={A,C,G,U}

Ribosome | Modulator

“Genetic Code” | “Signal Constellation”

H I D V

. . .

Histidine, Isoleucine, ..., Valine

Protein

A={Amino Acids} #A = 20

Codon 1 Codon 2 Codon np

Source

Channel encoder

(over Z4 or F4)

Channel

LECC

Over: Z20 F4xZ5

Mario Enrique Duarte Gonz´ alez 2015 SP Coding and Information School

Thank you

Mario Enrique Duarte Gonz´ alez 2015 SP Coding and Information School