Description

D. melanogaster transcripts annotated by FlyBase were aligned against the D. kikkawai genome assembly using a translated BLAT search. The thicker boxes denote the coding regions within the transcripts and the thinner boxes denote the untranslated regions.

Methods

D. melanogaster transcripts were mapped against the D. kikkawai genome assembly using BLAT with the following parameters: -q=rnax -t=dnax -mask=lower

The transcript alignments are analyzed by pslReps to identify the best alignments within the genome assembly that have a minimum alignment ratio of 0.25 (-minAli=0.25). The alignments are then filtered by pslCDnaFilter using the following parameters:

  -minId=0.35 -minCover=0.15 -localNearBest=0.010 -minQSize=20
  -ignoreIntrons -repsAsMatch -ignoreNs -bestOverlap

References

Kent WJ. BLAT--the BLAST-like alignment tool. Genome Res. 2002 Apr;12(4):656-64.