| 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 ge … MAKER is an easy-to-configure, portable genome [[:Category%253AAnnotation|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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| GMOD Malaysia 2014/MAKER Tutorial + , MAKER + , MAKER Tutorial 2010 + , MAKER Tutorial 2011 + , MAKER Tutorial 2012 + | Has topic |
| WebApollo + , WebApollo2 + | Interacts with |
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