MAKER is a portable and easily configurable genome annotation pipeline. Its purpose is to allow investigators to independently annotate eukaryotic genomes and create genome databases.

One of the great ironies of the DNA sequencing revolution is that genome annotation, not genome sequencing, has become the bottleneck in genomics today. New genomes are being sequenced at a far faster rate than they are being annotated. Tools to manage and analyze gene annotations are in great demand as more genomes are sequenced and published. Annotation management and comparison at the whole-genome scale is often restricted to analyses of basic traits. Although simple statistics are useful, they don’t move beyond the amino acid sequences to take into account other aspects of the annotations such as similarities in intron-exon structures and patterns of alternative splicing.

The Yandell lab has been working on an easy-to-use genome annotation pipeline called MAKER (yandell.topaz.genetics.utah.edu/cgi-bin/maker_license.cgi). The goal is to provide teams without extensive bioinformatics expertise the means to independently annotate genomes, with the option to distribute the results to the larger biomedical community. MAKER introduces new measures to evaluate changes to annotations across releases, such as Annotation Turnover, and Annotation Edit Distance. The other new measure that moves beyond state of the art quantifies the complexity of alternative splicing, called Splice Complexity. It offers two classes of analyses intra-genome comparisons of annotations that track and summarize genome-wide changes in annotations from release to release, and inter-genome comparisons that compare and contrast the annotations of different genomes to another. Practical issues such as completeness and usability are also taken into account.

Generating Revenue

• MAKER identifies repeats, aligns ESTs and proteins to a genome, produces ab initio gene predictions, and automatically synthesizes these data into gene annotations having evidence-based quality indices.
• MAKER is easily trainable.
• The outputs of preliminary runs are used to automatically retrain its gene-prediction algorithm, producing higher-quality gene-models on subsequent runs.
• The inputs for MAKER are minimal, and its outputs can be used to create a GMOD database.
• The outputs can be viewed in the Apollo Genome browser, which gives it an easy means to annotate, view, and edit individual contigs and BACs without the overhead of a database.

Eilbeck, K et al. “Quantitative measures for the management and comparison of annotated genomes.” BMC bioinformatics vol. 10 67. 23 Feb. 2009, doi:10.1186/1471-2105-10-67

Cantarel, BL et al. “MAKER: an easy-to-use annotation pipeline designed for emerging model organism genomes.” Genome res vol. 18,1 (2008): 188-96. doi:10.1101/gr.6743907

Campbell, MS et al. “Genome Annotation and Curation Using MAKER and MAKER-P.” Curr protocols in bioinformatics vol. 48 4.11.1-39. 12 Dec. 2014, doi:10.1002/0471250953.bi0411s48

Aaron Duffy
(801) 585-1377
aaron.duffy@utah.edu