title: 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.
abstract: BACKGROUND
  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.
  
  
  RESULTS
  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) comparative distribution across the neighborhood of orthologous genes. GREAM successfully short-listed a repeat element (MER20) known to contain functional motifs. In other case studies, we could use GREAM to short-list repetitive elements in the azoospermia factor a (AZFa) region of the human Y chromosome and those around the genes associated with rat liver injury. GREAM could also identify five over-represented repeats around some of the human and mouse transcription factor coding genes that had conserved expression patterns across the two species.
  
  
  CONCLUSIONS
  GREAM has been developed to provide an impetus to research on the role of repetitive sequences in mammalian genomes by offering easy selection of more interesting repeats in various contexts/regions. GREAM is freely available at http://resource.ibab.ac.in/GREAM/.
authors.affiliation: Institute of Bioinformatics and Applied Biotechnology (IBAB), Biotech Park, Electronic City, Bengaluru (Bangalore), 560100, Karnataka state, India; Manipal University, Manipal, 576104, Karnataka state, India.
authors.forename: Darshan Shimoga
authors.initials: DS
authors.lastname: Chandrashekar
authors.affiliation: Institute of Bioinformatics and Applied Biotechnology (IBAB), Biotech Park, Electronic City, Bengaluru (Bangalore), 560100, Karnataka state, India; Manipal University, Manipal, 576104, Karnataka state, India.
authors.forename: Poulami
authors.initials: P
authors.lastname: Dey
authors.affiliation: Institute of Bioinformatics and Applied Biotechnology (IBAB), Biotech Park, Electronic City, Bengaluru (Bangalore), 560100, Karnataka state, India; Shodhaka Life Sciences Pvt. Ltd., IBAB, Biotech Park, Bengaluru (Bangalore), 560100, Karnataka state, India.
authors.forename: Kshitish K
authors.initials: KK
authors.lastname: Acharya
mesh_terms: D000818:Animals; D002874:Chromosome Mapping; D003201:Computers; D004251:DNA Transposable Elements; D006801:Humans; D020407:Internet; D008322:Mammals / Q000235:genetics*; D011401:Promoter Regions, Genetic / Q000235:genetics; D012091:Repetitive Sequences, Nucleic Acid; D012984:Software; D013045:Species Specificity
chemical_list: D004251:DNA Transposable Elements