Feb 28, 2014

Genomic Repeat Element Analyzer for Mammals (GREAM)

BioRxiv : the Preprint Server for Biology
Darshan Shimoga ChandrashekarKshitish K Acharya

Abstract

Background: Understanding the mechanism behind the transcriptional regulation of genes is still a challenge. Recent findings indicate that the genomic repeat elements (such as LINES, SINES and LTRs) could play an important role in the transcription control. Hence, it is important to further explore the role of genomic repeat elements in the gene expression regulation, and perhaps in other molecular processes. Although many computational tools exists for repeat element analysis, almost all of them simply identify and/or classifying the genomic repeat elements within query sequence(s); none of them facilitate identification of repeat elements that are likely to have a functional significance, particularly in the context of transcriptional regulation. Result: We developed the ‘Genomic Repeat Element Analyzer for Mammals’ (GREAM) to allow gene-centric analysis of genomic repeat elements in 17 mammalian species, and validated it by comparing with some of the existing experimental data. The output provides a categorized list of the specific type of transposons, retro-transposons and other genome-wide repeat elements that are statistically over-represented across specific neighborhood regions of query genes. The position and frequenc...Continue Reading

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Mentioned in this Paper

Short Interspersed Nucleotide Elements
Positioning Attribute
Transcriptional Regulation
Classification
Genome
Genes
Transcription, Genetic
Research Personnel
Molecular_function
Genomics

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