Difference between revisions of "MAKER"

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{{ :MAKER/tool_data | template = Template:ToolDisplay }}
 
{{ :MAKER/tool_data | template = Template:ToolDisplay }}
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{{Tool data
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|name=MAKER
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|full name=
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|status=mature
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|dev=active
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|support=active
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|type=Genome Annotation
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|platform=linux, os x, unix
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|about=MAKER is a 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]].
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Additional MAKER options and capabilities include:
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* 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.
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* MAKER is <abbr title="message-passing interface">MPI</abbr>-capable for rapid parallelization across computer clusters.
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* 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]].
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MAKER comes with sample data for testing purposes.  See the <tt>/data</tt> directory in the download.
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|release date=2008
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|open source=Caveats apply
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|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
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|language=Perl
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|input=[[GFF3]], [[Glossary#FASTA|FASTA]]
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|output=[[GFF3]], [[Glossary#FASTA|FASTA]]
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|audience=private
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|logo=MAKERLogo.png
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|screenshot=[[File:MAKER_Apollo_view.jpg|none|thumb|500px|View of [[MAKER]] annotations in the [[Apollo]] genome annotation curation tool. Supporting evidence is shown in the upper dark panel. Gene annotations are shown in the blue panel.]]
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|survey link=MAKER
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|mail={{MailingListsFor|MAKER}}
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Support for MAKER is provided on a [http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org mailing list], and through a Trac-based [http://malachite.genetics.utah.edu/projects/maker/wiki wiki], [http://malachite.genetics.utah.edu/projects/maker/report bug tracker] and [http://malachite.genetics.utah.edu/projects/maker/browser code browser].
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|contact email=[mailto:carson.holt@genetics.utah.edu Carson Holt], [bmoore@genetics.utah.edu Barry Moore]
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|papers=
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*MAKER2: an annotation pipeline and genome-database management tool for second-generation genome projects. <ref name=PMID:22192575 />
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*MAKER: an easy-to-use annotation pipeline designed for emerging model organism genomes. <span class="Z3988" title="ctx_ver=Z39.88-2004&amp;rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&amp;rfr_id=info%3Asid%2Focoins.info%3Agenerator&amp;rft.genre=article&amp;rft_id=info%3Apmid%2F18025269">PMID:18025269</span> <ref name=PMID:18025269/>
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|presentations=* [[:Image:MAKERSMBE2009.pdf|MAKER—the easy-to-use genome annotation pipeline]], presented by Mark Yandell at the [http://ccg.biology.uiowa.edu/smbe/symposia.php?action=view&sym_ID=27 SMBE 2009 GMOD Workshop].
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|tutorials=;[[MAKER Tutorial]]
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:taught as part of the [[2013 GMOD Summer School]]
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|getting started preamble=We recommend that users read the MAKER paper [below] and the README file included with the download before installing and using MAKER.
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|req=* Perl 5.8.0 or higher
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* [[BioPerl]] 1.6 or higher.
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* [http://blast.wustl.edu WU-BLAST] 2.0 or higher or [http://www.ncbi.nlm.nih.gov/ NCBI-BLAST] 2.2.X or higher
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* [http://www.repeatmasker.org/ RepeatMasker] 3.1.6 or higher
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** RepeatMasker requires a repeat library, available from [http://www.girinst.org/repbase/index.html Repbase].
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* [http://www.animalgenome.org/bioinfo/resources/manuals/exonerate/ Exonerate] 1.4 or higher.
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Optional extras:
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* [http://korflab.ucdavis.edu/software.html SNAP] version 2009-02-03 or higher (for eukaryotic genomes).
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* [http://augustus.gobics.de Augustus] 2.0 or higher (for eukaryotic genomes)
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* [http://exon.biology.gatech.edu GeneMark-ES] (for eukaryotic genomes)
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* [http://www.softberry.com FGENESH] 2.6 or higher - requires licence (for eukaryotic genomes)
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* [http://exon.biology.gatech.edu GeneMarkS] (for prokaryotic genomes)
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|install=Please see the [http://www.yandell-lab.org/software/maker_install.html installation guide] or the README file in the download for instructions.
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|config=
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|doc=By default, MAKER runs on a single computer. A parallel version, mpi_maker, is also available. To run mpi_maker you will need a [http://en.wikipedia.org/wiki/Message_Passing_Interface message passing interface (MPI)] package installed on all participating computers; try [http://www.mcs.anl.gov/research/projects/mpich2/ MPICH2].  Remember to install MPICH2 with the <tt>--enable-sharedlibs</tt> flag set to the appropriate value .See the [http://www.mcs.anl.gov/research/projects/mpich2/documentation/index.php?s=docs MPICH2 Installer's Guide] for more information.
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=== Annotations ===
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The MAKER genome annotation pipeline generates several different types of annotations, including
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* ''Ab initio'' gene predictions from SNAP, Augustus, FGENESH, and GeneMark
 +
* Final gene models from MAKER
 +
* EST alignments from both EXONERATE and BLASTN
 +
* Protein alignments from EXONERATE and BLASTX
 +
* Repeats from RepeatMasker and the MAKER internal RepeatRunner
 +
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|dev ppl=Yandell Lab, Utah; Ian Korf (University of California Davis)
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|dev status=
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|dl tracking=
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|logo info=
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|see also=
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|extra=
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}}
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{{SemanticLink
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|linkurl=http://www.yandell-lab.org/software/maker.html
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|linktype=download
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}}
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{{SemanticLink
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|linkurl=http://yandell.topaz.genetics.utah.edu/cgi-bin/maker_license.cgi
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|linktype=source code
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}}
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{{SemanticLink
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|linkurl=http://www.yandell-lab.org/software/maker.html
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|linktype=website
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}}
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{{SemanticLink
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|linkurl=http://derringer.genetics.utah.edu/cgi-bin/MWAS/maker.cgi
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|linktype=public server
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|linktitle=MAKER Web Annotation Server
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|linkdesc=online version of the MAKER tool
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}}
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{{SemanticLink
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|linkurl=http://hymenopteragenome.org/ant_genomes/
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|linktype=wild urls
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|linktitle=Ant Genomes Portal
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|linkdesc=The ant genomes were annotated using MAKER.
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}}
  
 
[[Category:GMOD Components]]
 
[[Category:GMOD Components]]
 
[[Category:Annotation]]
 
[[Category:Annotation]]
 
[[Category:MAKER]]
 
[[Category:MAKER]]

Revision as of 22:13, 15 October 2013



MAKER logo
Status
  • Mature release
  • Development: active
  • Support: active
Resources


About MAKER

MAKER is a portable and easy to configure 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 or Apollo.

Additional MAKER options/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, GBrowse, or Apollo.

MAKER comes with sample data for testing purposes. See the /data directory in the download.

Visit the MAKER website.

Screenshots

View of MAKER annotations in the Apollo genome annotation curation tool. Supporting evidence is shown in the upper dark panel. Gene annotations are shown in the blue panel.

Downloads

  • MAKER is available as a compressed TAR file from the MAKER website.


Using MAKER

We recommend that users read the MAKER paper [below] and the README file included with the download before installing and using MAKER.

System Requirements

Optional extras:

  • SNAP version 2009-02-03 or higher (for eukaryotic genomes).
  • Augustus 2.0 or higher (for eukaryotic genomes)
  • GeneMark-ES (for eukaryotic genomes)
  • FGENESH 2.6 or higher - requires licence (for eukaryotic genomes)
  • GeneMarkS (for prokaryotic genomes)

Installation

An online installation guide is coming soon; please see the README file in the download for instructions.

Documentation

By default, MAKER runs on a single computer. A parallel version, mpi_maker, is also available. To run mpi_maker you will need a message passing interface (MPI) package installed on all participating computers; try MPICH2. Remember to install MPICH2 with the --enable-sharedlibs flag set to the appropriate value .See the MPICH2 Installer's Guide for more information.

Annotations

The MAKER genome annotation pipeline generates several different types of annotations, including

  • Ab initio gene predictions from SNAP, Augustus, FGENESH, and GeneMark
  • Final gene models from MAKER
  • EST alignments from both EXONERATE and BLASTN
  • Protein alignments from EXONERATE and BLASTX
  • Repeats from RepeatMasker and the MAKER internal RepeatRunner

Publications, Tutorials, and Presentations

Publications on or mentioning MAKER

  • MAKER2: an annotation pipeline and genome-database management tool for second-generation genome projects. [1]
  • MAKER: an easy-to-use annotation pipeline designed for emerging model organism genomes. PMID:18025269 [2]

Tutorials

MAKER Tutorial
taught as part of the 2013 GMOD Summer School

Presentations

Contacts and Mailing Lists

Mailing List Link Description Archive(s)
MAKER maker-devel MAKER developers and users list. Google, Nabble (2010/05+)

Support for MAKER is provided on a mailing list, and through a Trac-based wiki, bug tracker and code browser.


MAKER Development

Development team

Yandell Lab, Utah; Ian Korf (University of California Davis)

See also

http://hymenopteragenome.org/ant_genomes/

Almost all the ant genomes listed were independently annotated with MAKER.

More on MAKER

See Category:MAKER



  1. ↑ Cite error: Invalid <ref> tag; no text was provided for refs named PMID:22192575
  2. ↑ Cite error: Invalid <ref> tag; no text was provided for refs named PMID:18025269

Raw tool data at MAKER/tool data

"wild urls" is not in the list of possible values (website, download, source code, public server, demo server, wild URL, documentation, publication, social media, other) for this property.

Retrieved from "http://gmod.org/mediawiki/index.php?title=MAKER&oldid=24706"
Facts about "MAKER"RDF feed
Available on platformlinux +, os x + and unix +
Has URLhttp://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 + and http://hymenopteragenome.org/ant_genomes/ +
Has descriptionMAKER is a easy-to-configure, portable gen … MAKER is a 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.

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. +, online version of the MAKER tool + and The ant genomes were annotated using MAKER. +
Has development statusactive +
Has download URLhttp://yandell.topaz.genetics.utah.edu/cgi-bin/maker_license.cgi +
Has input formatGFF3 + and FASTA +
Has licenceGNU GPL (for academics) +, Artistic License 2.0 (for academics) + and custom license for commercial usage +
Has logoMAKERLogo.png +
Has output formatGFF3 + and FASTA +
Has software maturity statusmature +
Has support statusactive +
Has titleMAKER Web Annotation Server + and Ant Genomes Portal +
Has topicMAKER +
Has websitehttp://www.yandell-lab.org/software/maker.html +
Is open sourceCaveats apply +
Link typedownload +, source code +, website + and public server +
Release date2008 +
Tool functionality or classificationGenome Annotation +
Written in languagePerl +
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 + and MAKER#http://hymenopteragenome.org/ant_genomes/ +