GenSAS: An Easy-to-Use, Web-Based Solution for Specialty Crop Genome Annotation

As a result of reduced sequencing costs and increased federal funding to support specialty crop research, many horticultural crop genomes are in the process of being sequenced. Obtaining sequence data is relatively easy compared to determining the biological function encoded by the DNA or RNA sequence. In order for the sequence to be meaningful for researchers, structural and functional annotation needs to be performed to identify gene models and protein functions, respectively. The Genome Sequence Annotation Server (GenSAS) is a web-based annotation platform that packages command line annotation tools under one easy-to-use interface. The GenSAS walks researchers through each step of the annotation process and provides instructions and hints as each step progresses. These steps include: uploading of genomic sequence; uploading of supportive repeat library files, species-specific (or species-related) protein and transcript files; execution of repeat masking tools (including de novo repeat identification); execution of gene prediction tools; consensus gene prediction; manual structural annotation editing; functional annotation; and assistance with organization of files for final publication. The GenSAS is integrated with the popular JBrowse genome browser for feature visualization, and manual curation of structure and function is provided by an integrated Web Apollo interface.  The Genome Sequence Annotation Server was designed with researchers as the target user group and based on feedback, is an easy-to-use, customizable, online DNA annotation pipeline that allows users with little computer science knowledge to create a custom DNA annotation for their sequence(s) of interest.