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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
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, Online J Bioinformatics, 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