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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, 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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