3-way CDS alignments - D. melanogaster, D. simulans (consensus), D. yakuba

3-way CDS alignments - D. melanogaster, D. simulans (6 lines), D. yakuba

Please cite the following for the use of these CDS alignments or any use of the D. simulans or D. yakuba syntenic assemblies:

Begun, D.J., A.K. Holloway, K.S. Stevens, et al. 2007. Population genomics: whole-genome analysis of polymorphism and divergence in Drosophila simulans. PLoS Biology 5:e310.*


* annotation V4.2 of D. melanogaster
* alignments are based on the syntenic assemblies of D. simulans & D. yakuba
  - DPGP
* gene models for D. simulans and D. yakuba checked for:
  - initiation codon at the D. melanogaster start site
  - canonical splice junctions
  - no premature termination
  - termination at the D. melanogaster termination position
* the first set of alignments use a consensus D. simulans sequence
  - uses the most frequent codon from the 6 genomic D. simulans lines
  - any ambiguous codons become "NNN"
* D. yakuba sequence is included if data were available

For Chuck:
Tarball of autosomal VMA files for 3 African lines

For Angela:
Expression variation excel spreadsheet