Sim4cc D. mel Transcripts Track Settings

Sim4cc Alignment of D. melanogaster Transcripts (All Genes and Gene Prediction Tracks)

Display mode:

Alignment Gap/Insertion Display Options Help on display options
	Draw double horizontal lines when both genome and query have an insertion
	Draw a vertical purple line for an insertion at the beginning or end of the query, orange for insertion in the middle of the query

Display data as a density graph:

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Description

D. melanogaster transcripts from FlyBase were aligned against the D. biarmipes genome assembly using sim4cc.

Methods

D. melanogaster transcripts were mapped against the D. biarmipes genome assembly with blastn. For each protein, the region surrounding the best blastn hit is identified and the corresponding transcript is aligned against this genomic region with sim4cc using default parameters.

References

Zhou L, Pertea M, Delcher AL, Florea L. Sim4cc: a cross-species spliced alignment program. Nucleic Acids Res. 2009 Jun;37(11):e80.