Drosophila melanogaster (Apr 2006) fruit fly (dm3/BDGP R5) genome assembly

The files listed below are formatted for visualization in the Integrated Genome Browser, available from BioViz.org.

Annotation (bed) and alignment (psl) files (if available) were downloaded from the UCSC Genome Bioinformatics Table Browser. Each file is named for its corresponding table in the UCSC Genome database. See the annots.xml meta-data file in this directory for details.

Files with extension .gz were compressed and indexed using bgzip and tabix tools from htslib.org.

The file named D_melanogaster_Apr_2006.2bit contains sequence data and is from the UCSC Genome Bioinformatics Web site. To convert a .2bit to fasta, use twoBitToFa. The file genome.txt lists sequences and their sizes and was made from D_melanogaster_Apr_2006.2bit sequence file using twoBitInfo.

Both twoBitInfo and twoBitToFa are available from http://hgdownload.cse.ucsc.edu/admin/exe/.

	Name	Last modified	Size	Description
	Parent Directory		-
	D_melanogaster_Apr_2006.2bit	2023-06-16 13:41	42M	Sequence data in blat 2bit format
	D_melanogaster_Apr_2006_all_est.psl.gz	2023-06-16 13:41	22M	PSL (alignments) blat output file
	D_melanogaster_Apr_2006_all_est.psl.gz.tbi	2023-06-16 13:41	97K	Tabix index file
	D_melanogaster_Apr_2006_all_mrna.psl.gz	2023-06-16 13:41	2.7M	PSL (alignments) blat output file
	D_melanogaster_Apr_2006_all_mrna.psl.gz.tbi	2023-06-16 13:41	62K	Tabix index file
	D_melanogaster_Apr_2006_refGene.bed.gz	2023-06-16 13:41	1.1M	Data from UCSC refGene table
	D_melanogaster_Apr_2006_refGene.bed.gz.tbi	2023-06-16 13:41	58K	Tabix index file
	annots.xml	2023-06-16 13:41	1.4K	Annotation and data file list
	dm3-blacklist.v2.bed.gz	2023-06-16 13:41	2.4K	Annotation or junction file
	dm3-blacklist.v2.bed.gz.tbi	2023-06-16 13:41	2.9K	Tabix index file
	genome.txt	2023-06-16 13:41	228	Chromosome lengths and assembly information