MAKER

We have developed a portable and easily configurable genome annotation pipeline
called MAKER. Its purpose is to allow investigators to independently annotate
eukaryotic genomes and create genome databases. 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 also easily trainable: Outputs of preliminary runs are
used to automatically retrain its gene-prediction algorithm, producing
higher-quality gene-models on subsequent runs. MAKER's inputs are minimal, and
its outputs can be used to create a GMOD database. Its outputs can also be viewed
in the Apollo Genome browser; this feature of MAKER provides an easy means to
annotate, view, and edit individual contigs and BACs without the overhead of a
database. As proof of principle, we have used MAKER to annotate the genome of the
planarian Schmidtea mediterranea and to create a new genome database, SmedGD. We
have also compared MAKER's performance to other published annotation pipelines.
Our results demonstrate that MAKER provides a simple and effective means to
convert a genome sequence into a community-accessible genome database. MAKER
should prove especially useful for emerging model organism genome projects for
which extensive bioinformatics resources may not be readily available.

MAKER: an easy-to-use annotation pipeline designed for emerging model organism genomes.

MAKER tool is an annotation pipeline for eukaryotic and prokaryotic genomes. One can view the output of MAKER in the Apollo Genome browser.

MAKER

Topic

Detail

Publications

Download and documentation