GC-Profile 2.0: an extended web server for the prediction and visualization of CpG islands

Bioinformatics. 2022 Mar 4;38(6):1738-1740. doi: 10.1093/bioinformatics/btab864.

Abstract

Summary: Due to the spontaneous deamination of 5'-methylcytosine into thymine, the number of CpG dinucleotides is less than expected in vertebrate genomes. Exceptionally, there are a large number of CpG dinucleotides clustered at certain genomic loci, known as CpG islands (CGIs), where CpG dinucleotides are free from methylation. Identification of CGIs is of great significance in the field of genomics and epigenetics because they can serve as important gene markers or regulatory elements. Here, GC-Profile 2.0 has been presented as a newly extended application for CGIs detection and visualization. Based on a benchmark test of assembled sequences, GC-Profile 2.0 has shown better overall performance compared with other four popular methods. In addition, cumulative CpG profile, a visualization tool of CpG content variation, is also proposed to intuitively display the change trend of CpG content.

Availability and implementation: GC-Profile 2.0 is freely available at http://tubic.org/GC-Profile2.

Supplementary information: Supplementary data are available at Bioinformatics online.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • CpG Islands
  • DNA Methylation
  • Epigenesis, Genetic
  • Genome*
  • Genomics* / methods