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MAKER
Available on platform linux  + , os x  + , unix  +
Has URL 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  +
Has description online version of the MAKER tool  + , The ant genomes were annotated using MAKER.  + , MAKER is an easy-to-configure, portable geMAKER 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  +
Has development status active  +
Has input format [[GFF3]]  + , [[Glossary#FASTA|FASTA]]  +
Has licence [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  +
Has logo MAKERLogo.png  +
Has output format [[GFF3]]  + , [[Glossary#FASTA|FASTA]]  +
Has software maturity status mature  +
Has support status active  +
Has title MAKER Web Annotation Server  + , Ant Genomes Portal  + , MAKER-P  + , A beginner's guide to eukaryotic genome annotation  +
Has topic MAKER +
Is open source Caveats apply  +
Link type download  + , source code  + , website  + , public server  + , publication  + , other  +
Release date 2008  +
Tool functionality or classification Genome Annotation  +
Written in language Perl  +
Has queryThis property is a special property in this wiki. MAKER + , MAKER + , MAKER + , MAKER + , MAKER + , MAKER + , MAKER + , MAKER + , MAKER + , MAKER +
Has improper value forThis property is a special property in this wiki. Link type  +
Categories GMOD Components  + , MAKER  + , Annotation  + , GMOD Component  + , SemanticLink  +
Modification dateThis property is a special property in this wiki. 2 February 2014 21:53:48  +
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#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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