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OJBTM
Online Journal of Bioinformatics

  

Volume 10 (1):40-50, 2009.


In silico identification of tandem inter/intra-generic genetic elements (TIGE) using a random nucleotide generating Perl program:

A potential approach for locating structure-function regions of recently sequenced genomes.

 

 Jha PK, Stashenko P.

 

Department of Cytokine Biology, The Forsyth Institute, Harvard Medical School Affiliate in Oral and Craniofacial Science, 140 Fenway, Boston, MA 02115, USA.

 

 

 

ABSTRACT

 

Jha PK, Stashenko P., In silico identification of tandem inter/intra-generic genetic elements (TIGE) using a random nucleotide generating Perl program: A potential approach for locating structure-function regions of recently sequenced genomes, Onl J Bioinform., 10 (1):40-50, 2009. In an attempt to relate gene sequences to a specific function by a simple bioinformatics approach, a few basic programs were written in open source programming language Perl. These programs generate random nucleotides of desired length and create small text databases. A comparison of multiple 600 random nucleotides query sequence with public databases identified identity with several short 20+ nucleotide sequences. Query sequences whose adjoining 20+ nucleotide blocks showed at least near-contiguous identity with another non-duplicate database sequence were considered relevant. These tandem sequences were termed TIGE (tandem inter/intra-generic genetic elements). Several TIGE were identified including one spanning 58 nucleotides in sequences of human chromosome 11p14.4, rice chromosome 2 and mouse importin 8 mRNA. Comparative analysis revealed query sequence identity to modular regulatory sequences, gene for initiation of chromosome replication and microsatellite DNA. Identity in same region of query sequence to three different human chromosomes, 2, 18 and X, suggested their genetic material exchange. TIGE may represent short DNA sequences which are hallmark of evolution. The approach taken in this investigation identifies them and other yet unknown regulatory elements or sequences that share structure-function properties of scientific interest.

 

Keywords: random nucleotide, Perl, structure function region, tandem element


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