Description

D. melanogaster proteins from FlyBase were aligned against the D. ananassae gneome assembly using Spaln2 with cross-species parameters.

Methods

The list of genes that aligned to each contig were determined by the best hit in the D. melanogaster blastx track at each genomic locus. mRNA transcripts from each of these genes were aligned against the contig using Spaln2 with cross-species parameters optimized for D. melanogaster: (-Tdromel -yX -yS).

References

Iwata H., and Gotoh, O. Benchmarking spliced alignment programs including Spaln2, an extended version of Spaln that incorporates additional species-specific features. Nucleic Acids Research. 2012, 109