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modENCODE

The National Human Genome Research Institute model organism ENCyclopedia Of DNA Elements

The modENCODE Project will try to identify all of the sequence-based functional elements in the Caenorhabditis elegans and Drosophila melanogaster genomes.

modENCODE data file formats and quick start guide

Most of the links in the integrative worm paper companion page bring you to a modMine 'Submission summary page'.

This summary page provides all the available information about the submission and resulting data. There are 2 choices for getting straight to the data:

  1. Click on the "GBrowse tracks" link - this will load a new window with gbrowse displaying the data as a track. You can use Gbrowse to navigate the dataset, compare with other datasets, export track views and customize your viewing preferences.
  2. There is a list of "Data files" > right click and save as to download the data file. This can be used as input to your own analysis and can always be viewed later using gbrowse at modencode.org, wormbase or ucsc.

Summary of accessing modencode data and modmine resources

modENCODE data can be viewed using several different options. It can be viewed using the modencode, WormBase and UCSC gbrowsers. Using any of the above options enables you to visually compare a range of experiment conditions by uploading (or selecting) data files of interest. modENCODE data is available in GFF3 and wiggle track (.wig) formats, depending on the source experiment. Using the gbrowse / modmine interfaces, it is also possible to export some subsets of data into other formats such as high resolution .pdf for other purposes.

GFF3 data files

GFF = Generic Feature Format, and GFF3 is the most recent version. GFF3 files are plain text tab-delimited files used to represent genomic data. GFF3 files are commonly used to represent alignments, transcripts, genes, operons and numerous other features. There is a standardized format for columns, definitions and metadata that make a GFF3 file. More detailed information about GFF3 is available at

WIG data files

WIG = wiggle track format WIG files are used to display genomic data in a track format. WIG files are commonly used to display transcriptome data, GC percent and probability scores as values for a genomic position. More detailed information about WIG format files is available at