Description

D. melanogaster proteins annotated by FlyBase were aligned against the D. takahashii genome assembly using Spaln2 with cross-species parameters.

Methods

D. melanogaster proteins were mapped against the D. takahashii genome assembly with tblastn. For each protein, the region surrounding the best tblastn hit is identified and each protein is re-aligned against this genomic region with Spaln2 using cross-species parameters optimized for D. melanogaster: (-Tdromel -yX).

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