Rxivist logo

Rxivist combines preprints from bioRxiv with data from Twitter to help you find the papers being discussed in your field. Currently indexing 64,995 bioRxiv papers from 288,045 authors.

EpiAlignment: alignment with both DNA sequence and epigenomic data

By Jia Lu, Xiaoyi Cao, Sheng Zhong

Posted 27 Feb 2019
bioRxiv DOI: 10.1101/562199 (published DOI: 10.1093/nar/gkz426)

Comparative epigenomics, by subjecting both epigenome and genome to interspecies comparison, has become a powerful approach to reveal regulatory features of the genome. Thus elucidated regulatory features surpassed the information derived from comparison of genomic sequences alone. Here, we present EpiAlignment, a web-based tool to align genomic regions with both DNA sequence and epigenomic data. EpiAlignment takes DNA sequence and epigenomic profiles derived by ChIP-seq, DNase-seq, or ATAC-seq from two species as input data, and outputs the best semi-global alignments. These alignments are based on EpiAlignment scores, computed by a dynamic programming algorithm that accounts for both sequence alignment and epigenome similarity. For timely response, the EpiAlignment web server automatically initiates up to 140 computing threads depending on the size of user input data. For users' convenience, we have pre-compiled the comparable human and mouse epigenome datasets in matched cell types and tissues from the Roadmap Epigenomics and ENCODE consortia. Users can either upload their own data or select pre-compiled datasets as inputs for EpiAlignment analyses. Results are presented in graphical and tabular formats where the entries can be interactively expanded to visualize additional features of these aligned regions. EpiAlignment is available at https://epialign.ucsd.edu/.

Download data

  • Downloaded 214 times
  • Download rankings, all-time:
    • Site-wide: 44,364 out of 64,995
    • In bioinformatics: 5,067 out of 6,434
  • Year to date:
    • Site-wide: 20,804 out of 64,995
  • Since beginning of last month:
    • Site-wide: 60,562 out of 64,995

Altmetric data


Downloads over time

Distribution of downloads per paper, site-wide


Sign up for the Rxivist weekly newsletter! (Click here for more details.)


News