Physical Mapping and Sequence Assembly

Introduction

The goal of the Human Genome Project is the determination of the location of the human genes on the DNA and the sequencing (the determination of the sequence of nucleotides A,C,G and T) of the entire human genome. In total, the human genome contains about 3 billion letters distributed over 23 chromosomes. Maps that reflect the actual distance in base pairs are callled physical maps. Physical maps are powerful tools for localization and isolation of genes, studying the organization and evolution of genomes and as a preparatory step for efficient sequencing.

The procedure of physical mapping coarsely divides into two steps (see figure below): First large pieces of DNA (contigs), a library of cloned fragments are ordered according to their position in the genome. Different experimental techniques are used to do that. Roughly, these are clone-probe hybridization mapping, restriction mapping, radiation-hybrid mapping and optical mapping. Here we will focus on Mapping using hybridization data [1] [2] [3]. Second the cloned fragments are cut by restriction enzymes, smaller DNA fragments are obtained which are sequenced in detail (shotgun-sequencing), and the overall sequence in detail is obtained by Sequence Assembly.