The IGS Standard Operating Procedure for Automated Prokaryotic Annotation

Stand Genomic Sci. 2011 Apr 29;4(2):244-51. doi: 10.4056/sigs.1223234. Epub 2011 Apr 25.


The Institute for Genome Sciences (IGS) has developed a prokaryotic annotation pipeline that is used for coding gene/RNA prediction and functional annotation of Bacteria and Archaea. The fully automated pipeline accepts one or many genomic sequences as input and produces output in a variety of standard formats. Functional annotation is primarily based on similarity searches and motif finding combined with a hierarchical rule based annotation system. The output annotations can also be loaded into a relational database and accessed through visualization tools.

Keywords: BER; Ergatis; Glimmer; HMM; IGS Annotation Engine; Institute for Genome Sciences; Manatee; annotation pipeline; functional annotation; microbial genomics; pFunc; prokaryotic genomics; structural annotation.