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GREAM

GREAM

GREAM (Genomic Repeat Element Analyzer for Mammals) is a tool to select, screen, and analyze genomic repeats in mammals that are likely to be important.

GREAM offers the following listings and analyzes:
1. Produce a categorized list of a wide range of statistically over- or under-reperensented repeated elements, and specific types, such as, for example, transposons, retro-transposons.
2. Enrichment within a specied region of a chromosome.
3. comparative distribution across the neighborhood of orthologous genes.

Topic

Genomics; Sequence composition, complexity and repeats; Sequence analysis

Details

  • Operation: Repeat sequence analysis
  • Software interface: Web user interface
  • Language: Perl
  • Operating system: Linux; Mac OS X; Microsoft Windows
  • License: Not stated
  • Cost: Free
  • Version name: -
  • Credit: Department of Electronics and Information Technology (DeitY), Government of India, under ‘Centre of Excellence for Research and Teaching in Bioinformatics.
  • Contact: kshitish _at_ ibab.ac.in
  • Collection: -

Publications

Chandrashekar DS, Dey P, Acharya KK "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 2015; 10(7):e0133647 https://doi.org/10.1371/JOURNAL.PONE.0133647
PMID: 26208093
PMCID: PMC4514817


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