GMOD

MAKER

MAKER logo

Status

Licence

GNU GPL (for academics), Artistic License 2.0 (for academics), custom license for commercial usage

Resources

Facts about “MAKER”

Available on platform linux +, os x + and unix +
Has URL http://www.yandell-lab.org/software/maker.html +, http://yandell.topaz.genetics.utah.edu/cgi-bin/maker_license.cgi +, https://www.e-biogenouest.org/resources/48 +, http://www.yandell-lab.org/software/maker-p.html +, http://derringer.genetics.utah.edu/cgi-bin/MWAS/maker.cgi + and http://hymenopteragenome.org/ant_genomes/ +
Has description MAKER is an easy-to-configure, portable ge … MAKER is an easy-to-configure, portable genome annotation pipeline. MAKER allows smaller eukaryotic genome projects and prokaryotic genome projects to annotate their genomes and to 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 with evidence-based quality values. MAKER is also easily trainable: outputs of preliminary runs can be used to automatically retrain its gene prediction algorithm, producing higher quality gene-models on subsequent runs. MAKER's inputs are minimal. Its outputs are in GFF3 or FASTA format, and can be directly loaded into Chado, GBrowse, JBrowse, WebApollo or Apollo.

For those annotating novel plant genomes, the MAKER-P pipeline is designed to make the annotation tractable for small groups with limited bioinformatics experience and resources, and faster and more transparent for large groups with more experience and resources. The MAKER-P pipeline generates species-specific repeat libraries, as well as structural annotations of protein coding genes, non-coding RNAs, and pseudogenes. The MAKER-P website has more information on the additional protocols for plant genome annotation.

Additional MAKER options and capabilities include:

  • Map old annotation sets on to new assemblies.
  • Merge multiple legacy annotation sets into a consensus set of annotations.
  • Update existing annotations to take new evidence into account.
  • Tag pre-existing gene models with evidence alignments and quality control metrics to assist in downstream manual curation.
  • Use GFF3 pass-through to include both evidence alignments and predicted gene models from algorithms not natively supported by MAKER.
  • MAKER is MPI-capable for rapid parallelization across computer clusters.
  • You can also easily integrate raw InterProScan results into MAKER, which will identify protein domains; add GO functional categories; and help assign putative gene functions to genome annotations. This data then becomes accessible as part of the GFF3 output and can be loaded into a Chado database, JBrowse, GBrowse, WebApollo or Apollo.
MAKER comes with sample data for testing purposes. See the /data directory in the download. /data directory in the download. , Review article on eukaryotic genome annotation from the MAKER team. , MAKER with additional software for plant genome annotation , online version of the MAKER tool and The ant genomes were annotated using MAKER.
Has development status active +
Has input format GFF3 + and FASTA +
Has licence GNU GPL (for academics) +, Artistic License 2.0 (for academics) + and custom license for commercial usage +
Has logo MAKERLogo.png +
Has output format GFF3 + and FASTA +
Has software maturity status mature +
Has support status active +
Has title A beginner's guide to eukaryotic genome annotation +, MAKER-P +, MAKER Web Annotation Server + and Ant Genomes Portal +
Has topic MAKER +
Is open source Caveats apply +
Link type download +, source code +, website +, publication +, other + and public server +
Release date 2008 +
Tool functionality or classification Genome Annotation +
Written in language Perl +
Has subobjectThis property is a special property in this wiki. MAKER#http://www.yandell-lab.org/software/maker.html +, MAKER#http://yandell.topaz.genetics.utah.edu/cgi-bin/maker_license.cgi +, MAKER#https://www.e-biogenouest.org/resources/48 +, MAKER#http://www.yandell-lab.org/software/maker-p.html +, MAKER#http://derringer.genetics.utah.edu/cgi-bin/MWAS/maker.cgi + and MAKER#http://hymenopteragenome.org/ant_genomes/ +

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