The "Download" button will download the checked CRM records in one of a variety of formats. At present, REDfly supports the following options:
Sequences in multi-FASTA format. The FASTA header contains the following data:
Comma-separated list, one line per record. Fields are: "name", "species name", "gene_name", "flybase_id", "chromosome", "sequence"
Data in GFF version 3 format. The "attributes" field holds the CRM name ("ID="); database identifiers ("dbxref=") for FlyBase, PubMed (PMID), and REDfly; and the expression terms("Ontology_term="). Note that because TFBSs and CRMs are not strand-specific sequence features, no strand information is specified in the GFF file.
GBrowse Annotation Format
The format used by GBrowse to load local custom annotations. Newer versions of GBrowse (GBrowse2) use a modified version of this format. Downloads in this format will be included in the future. However, note that most GBrowse implementations can also accept custom annotations in GFFv3 format.
Data in BED format. File type “BED simple” downloads a four-column BED file (chrom, start, end, name) with no headers, suitable for direct analysis or for use with a genome browser. File type “BED browser” produces a eight-column BED file with additional header information to enable richer functionality when used with the UCSC Genome Browser. Default track name of “CRMs” or “TFBS” and default track description of “CRMs (or TFBSs) selected from REDfly” is specified.
NOTE: There is a current download limit of 1000 records. To download more results, use the check box to select all displayed records in the current “Search Results” page and download; then move to the next page and repeat; and so on. Future REDfly releases will allow direct downloading of the full search results.