GenSAS: A Web-Based Platform for Automated and Manual Curation of Genomic Sequence

Structural and functional annotation of genomic DNA can be complex when considering the quantity of tools required; the sequence of steps; the knowledge required to identify, correct and annotate genomic features; preparation of tool input files and conversion of file formats between them; the ability to interact with a UNIX-style command-line; and file preparation for final submission to an online genomic database.  Such complexity can be a limiting factor for some researchers and a challenge for students to learn. The Genome Sequence Annotation Server (GenSAS) was created to simplify the process of automated and manual annotation of genomic sequence by providing a simplified web interface and combines both automated and manual curation steps.  It is designed to annotate genomic sequence for the researcher and assist with training of students. GenSAS performs genome annotation by providing a web-based interface that walks the user through each step of annotation 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; and assistance with organization of files for final publication.  GenSAS is integrated with the popular JBrowse genome browser for feature visualization, and manual curation of structure and function is provided by an integrated WebApollo interface.  Currently GenSAS supports automated and manual structural annotation.  A more robust functional annotation step is forthcoming.