©1996-2019 All Rights Reserved. Online Journal of Bioinformatics . You may not store these pages in any form except for your own personal use. All other usage or distribution is illegal under international copyright treaties. Permission to use any of these pages in any other way besides the before mentioned must be gained in writing from the publisher. This article is exclusively copyrighted in its entirety to OJB publications. This article may be copied once but may not be, reproduced or re-transmitted without the express permission of the editors. This journal satisfies the refereeing requirements (DEST) for the Higher Education Research Data Collection (Australia). Linking:To link to this page or any pages linking to this page you must link directly to this page only here rather than put up your own page.
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.
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