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

The IGS Standard Operating Procedure for Automated Prokaryotic Annotation.

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Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA.


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.


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

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