In the FB2015_01 release of FlyBase the genome assembly of Drosophila simulans has been updated. The old release 1 mosaic assembly has been replaced by the assembly generated by Hu et al. and described in FBrf0220370 based on the w[501] strain and is designated as release 2.

In addition to the new release 2 assembly, the CAF1 generated annotations that have not changed since 2006 are being replaced by annotations generated by NCBI as part of their GNOMON annotation pipeline as described in this paper (http://www.ncbi.nlm.nih.gov/core/assets/genome/files/Gnomon-description.pdf).

We have maintained gene, transcript and protein symbol and IDs for GNOMON annotations identified by NCBI as corresponding to existing CAF1 annotations but many models have new identifiers. Due to the large differences between assemblies FlyBase is not providing a coordinate converter for this species. If you need to convert coordinates between the old and new assembly you can do so at the NCBI remap service (http://www.ncbi.nlm.nih.gov/genome/tools/remap).

As of February 17, 2015 bulk format gff3, gtf and fasta files are being made available on our ftp site (ftp://ftp.flybase.org/genomes/dsim/dsim_r2.01_FB2015_01/).