Jul 25, 2015

GREAM: A Web Server to Short-List Potentially Important Genomic Repeat Elements Based on Over-/Under-Representation in Specific Chromosomal Locations, Such as the Gene Neighborhoods, within or across 17 Mammalian Species

PloS One
Darshan Shimoga ChandrashekarKshitish K Acharya


Genome-wide repeat sequences, such as LINEs, SINEs and LTRs share a considerable part of the mammalian nuclear genomes. These repeat elements seem to be important for multiple functions including the regulation of transcription initiation, alternative splicing and DNA methylation. But it is not possible to study all repeats and, hence, it would help to short-list before exploring their potential functional significance via experimental studies and/or detailed in silico analyses. We developed the 'Genomic Repeat Element Analyzer for Mammals' (GREAM) for analysis, screening and selection of potentially important mammalian genomic repeats. This web-server offers many novel utilities. For example, this is the only tool that can reveal a categorized list of specific types of transposons, retro-transposons and other genome-wide repetitive elements that are statistically over-/under-represented in regions around a set of genes, such as those expressed differentially in a disease condition. The output displays the position and frequency of identified elements within the specified regions. In addition, GREAM offers two other types of analyses of genomic repeat sequences: a) enrichment within chromosomal region(s) of interest, and b) com...Continue Reading

  • References32
  • Citations


  • This paper may not have been cited yet.

Mentioned in this Paper

Real-Time Polymerase Chain Reaction
Genome-Wide Association Study
Short Interspersed Nucleotide Elements
Positioning Attribute
Transcriptional Regulation
Repetitive Region

Related Feeds

Alternative splicing

Alternative splicing a regulated gene expression process that allows a single genetic sequence to code for multiple proteins. Here is that latest research.

Related Papers

Mammalian Genome : Official Journal of the International Mammalian Genome Society
Hasan KhatibEui-Soo Kim
Genetics and Molecular Research : GMR
Melissa Nunes MiziaraM Elisabete J Amaral
© 2020 Meta ULC. All rights reserved