Novel algorithm to determine highly homologous segmental gemone duplication

Abstract

In the world of genomic research, projects aimed at revealing the complete sequence of a given genome are usually cumbersome and tedious. The major problem in these projects is that the long sequence of the genome should pass two processes; 1) randomly cutting it into a huge number of short DNA sequences known as Whole genome-shotgun reads (WGSRs ), 2) thereafter using computer programs to reconstruct the whole genome sequence. The main drawback during the reconstruction process is the small fragments that come from duplicated segment in the original genome. Segmental duplication is a well known phenomenon which refers to blocks of DNA sequence that exist in more than one copy in the genome. The objective of my project is to develop a Windows-based system that can efficiently analyze and delineate segmental duplications. in WGSRs databases. The main advantage of this system is its simplicity for users as well as capability to be used for any WGSRs database. Perl was used for developing this system because it is a very strong language in string processing and analysis. In addition, Perl has many bioinformatics modules that can facilitate programming for biological applications.