In search of genome annotation consistency: solid gene clusters and how to use them.
Maintaining consistency in genome annotations is important for supporting many computational tasks, particularly metabolic modeling. The SEED project has implemented a process that improves annotation consistencies across microbial genomes for proteins with conserved sequences and genomic context. In this research report, we describe this process and show how this effort has resulted in improvements to microbial genome annotations in the SEED. We also compare SEED annotation consistencies with other commonly used resources such as IMG (the Joint Genome Institute's Integrated Microbial Genomes system), RefSeq (the National Center for Biotechnology Information's Reference Sequence Database), Swiss-Prot (the annotated protein sequence database of the Swiss Institute of Bioinformatics, European Molecular Biology Laboratory and the European Bioinformatics Institute) and TrEMBL (Translated European Molecular Biology Laboratory nucleotide sequence data Library). Our analysis indicates that manual and computational efforts are paying off for the databases where consistency is a major goal.
Institute for Genomic Biology, MC-195, University of Illinois at Urbana-Champaign, 1206 W. Gregory Dr., Urbana, IL, 61801, USA. james2@illinois.edu.
James J
JJ
Davis
Institute for Genomic Biology, MC-195, University of Illinois at Urbana-Champaign, 1206 W. Gregory Dr., Urbana, IL, 61801, USA.|Department of Microbiology, University of Illinois at Urbana-Champaign, 601 S. Goodwin Ave., Urbana, IL, 61801, USA.
Gary J
GJ
Olsen
Fellowship for Interpretation of Genomes, 15W155 81st St., Burr Ridge, IL, 60527, USA.|Mathematics and Computer Science, Argonne National Laboratory, 9700 S. Cass Ave., Argonne, IL, 60439, USA.
Ross
R
Overbeek
Fellowship for Interpretation of Genomes, 15W155 81st St., Burr Ridge, IL, 60527, USA.
Veronika
V
Vonstein
Mathematics and Computer Science, Argonne National Laboratory, 9700 S. Cass Ave., Argonne, IL, 60439, USA.
Fangfang
F
Xia
Automatic annotation; Protein clusters