Assemblies of the resequenced genomes of the Drosophila strains described in McManus, C.J., Coolon, J.D., Eipper-Mains, J., Wittkopp, P.J. and Graveley, B.R. (2014) Evolution of Splicing Regulatory networks inDrosophila. Genome Research, in press.
The files included in this tar.gz contain the resequenced versions of the D. simulans (Tsimbazaza strain; Hollocher et al. 2000) and D. sechellia (Reference strain; 14021-0231.36) genomes, as well as genome from D. melanogaster strains zhr and z30 (McManus et al., 2014 (accepted)) in fasta format. Chain files are also included to convert coordinates on these genomes to those of the D. melanogaster reference version 3 (dm3), using the liftOver tool available on the UCSC genome browser website (http://hgdownload.soe.ucsc.edu/admin/exe/). Custom perl scripts are also included to convert coordinates from the D. simulans and D. sechellia genomes into dm3 coordinates (as this is a multi-step process). You must have the liftOver tool installed in your path to use these perl scripts. (Download here -> SplicingRegDivGenomes.zip).
Mod-seeker data analysis pipeline for high-throughput probing of RNA chemical modification, as described in Talkish, J, May, GE, Lin, Y, Woolford JL, Jr, and McManus CJ. (2014). Mod-seq: High-throughput sequencing for chemical probing of RNA structure. RNA (accepted).
The files included in this tar.gz contain mod-seeker analysis pipeline and test data (Download here ->Mod-seeker.tar ).