Description

This track shows the gene predictions from the Augustus program. The predictions are based on hints provided by the SPALN alignments of D. melanogaster proteins against the D. simulans genome assembly, as well as splice junction predictions and assembled transcripts derived from D. simulans RNA-Seq data.

References

Stanke M, Diekhans M, Baertsch R, Haussler D. Using native and syntenically mapped cDNA alignments to improve de novo gene finding. Bioinformatics. 2008 Mar 1;24(5):637-44. doi: 10.1093/bioinformatics/btn013.

Iwata H, Gotoh O. Benchmarking spliced alignment programs including Spaln2, an extended version of Spaln that incorporates additional species-specific features. Nucleic Acids Res. 2012 Nov 1;40(20):e161. doi: 10.1093/nar/gks708.

Haas BJ et al. De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis. Nat Protoc. 2013 Aug;8(8):1494-512.

Kovaka S, Zimin AV, Pertea GM, Razaghi R, Salzberg SL, Pertea M. Transcriptome assembly from long-read RNA-seq alignments with StringTie2. Genome Biol. 2019 Dec 16;20(1):278.