Description

RNA-seq reads generated by the modENCODE project for D. mojavensis were mapped against the D. mojavensis genome using TopHat2 and predicted transcripts are assembled using Cufflinks and CEM. Coding regions within the predicted transcripts are identified using TransDecoder. This collection of coding regions are aligned against the D. mojavensis genome using blastx followed by Spaln2.

Methods

Candidate coding regions in the collection of assembled D. mojavensis transcripts were identified using TransDecoder using the following parameters: -m 50, --search_pfam Pfam-A.hmm.

The collection of predicted D. mojavensis proteins were initially mapped against the D. mojavensis genome using BLASTX to identify regions of similarity. Spaln2 is then used to re-align each protein against their corresponding region with same-species parameters optimized for D. melanogaster: (-Tdromel -yS).

References

Hass B. TransDecoder (Finding Coding Regions Within Transcripts).

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

The RNA-Seq data were submitted by the modENCODE project. The original RNA-Seq dataset can be obtained from the NCBI GEO database under the accession number GSE28078.