Available on platform
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linux +
, os x +
, unix +
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Has URL
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http://www.yandell-lab.org/software/maker.html +
, http://yandell.topaz.genetics.utah.edu/cgi-bin/maker_license.cgi +
, http://derringer.genetics.utah.edu/cgi-bin/MWAS/maker.cgi +
, http://hymenopteragenome.org/ant_genomes/ +
, http://www.yandell-lab.org/software/maker-p.html +
, https://www.e-biogenouest.org/resources/48 +
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Has description
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online version of the MAKER tool +
, The ant genomes were annotated using MAKER. +
, MAKER is an easy-to-configure, portable ge … MAKER is an easy-to-configure, portable genome [[:Category:Annotation|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 [[Glossary#FASTA|FASTA]] format, and can be directly loaded into [[Chado]], [[GBrowse]], [[JBrowse]], [[WebApollo]] or [[Apollo]].
For those annotating novel plant genomes, the [http://www.yandell-lab.org/software/maker-p.html 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 [http://www.yandell-lab.org/software/maker-p.html 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 <abbr title="message-passing interface">MPI</abbr>-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 <tt>/data</tt> directory in the download.data</tt> directory in the download. +
, Review article on eukaryotic genome annotation from the MAKER team. +
, MAKER with additional software for plant genome annotation +
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Has development status
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active +
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Has input format
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[[GFF3]] +
, [[Glossary#FASTA|FASTA]] +
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Has licence
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[http://opensource.org/licenses/gpl-license GNU GPL (for academics)] +
, [http://opensource.org/licenses/artistic-license-2.0 Artistic License 2.0 (for academics)] +
, custom license for commercial usage +
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Has logo
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MAKERLogo.png +
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Has output format
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[[GFF3]] +
, [[Glossary#FASTA|FASTA]] +
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Has software maturity status
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mature +
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Has support status
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active +
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Has title
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MAKER Web Annotation Server +
, Ant Genomes Portal +
, MAKER-P +
, A beginner's guide to eukaryotic genome annotation +
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Has topic
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MAKER +
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Is open source
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Caveats apply +
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Link type
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download +
, source code +
, website +
, public server +
, publication +
, other +
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Release date
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2008 +
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Tool functionality or classification
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Genome Annotation +
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Written in language
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Perl +
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Has queryThis property is a special property in this wiki.
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MAKER +
, MAKER +
, MAKER +
, MAKER +
, MAKER +
, MAKER +
, MAKER +
, MAKER +
, MAKER +
, MAKER +
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Has improper value forThis property is a special property in this wiki.
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Link type +
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Categories |
GMOD Components +
, MAKER +
, Annotation +
, GMOD Component +
, SemanticLink +
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Modification dateThis property is a special property in this wiki.
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2 February 2014 21:53:48 +
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Has subobjectThis property is a special property in this wiki.
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MAKER#http://www.yandell-lab.org/software/maker.html +
, MAKER#http://yandell.topaz.genetics.utah.edu/cgi-bin/maker_license.cgi +
, MAKER#http://derringer.genetics.utah.edu/cgi-bin/MWAS/maker.cgi +
, MAKER#http://hymenopteragenome.org/ant_genomes/ +
, MAKER#http://www.yandell-lab.org/software/maker-p.html +
, MAKER#https://www.e-biogenouest.org/resources/48 +
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