Difference between revisions of "MAKER"
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{{ :MAKER/tool_data | template = Template:ToolDisplay }} | {{ :MAKER/tool_data | template = Template:ToolDisplay }} | ||
+ | |||
+ | {{Tool data | ||
+ | |name=MAKER | ||
+ | |full name= | ||
+ | |status=mature | ||
+ | |dev=active | ||
+ | |support=active | ||
+ | |type=Genome Annotation | ||
+ | |platform=linux, os x, unix | ||
+ | |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]]. | ||
+ | |||
+ | 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. | ||
+ | |release date=2008 | ||
+ | |open source=Caveats apply | ||
+ | |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 | ||
+ | |language=Perl | ||
+ | |input=[[GFF3]], [[Glossary#FASTA|FASTA]] | ||
+ | |output=[[GFF3]], [[Glossary#FASTA|FASTA]] | ||
+ | |audience=private | ||
+ | |logo=MAKERLogo.png | ||
+ | |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.]] | ||
+ | |survey link=MAKER | ||
+ | |mail={{MailingListsFor|MAKER}} | ||
+ | |||
+ | 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]. | ||
+ | |contact email=[mailto:carson.holt@genetics.utah.edu Carson Holt], [bmoore@genetics.utah.edu Barry Moore] | ||
+ | |papers= | ||
+ | *MAKER2: an annotation pipeline and genome-database management tool for second-generation genome projects. <ref name=PMID:22192575 /> | ||
+ | *MAKER: an easy-to-use annotation pipeline designed for emerging model organism genomes. <span class="Z3988" title="ctx_ver=Z39.88-2004&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rfr_id=info%3Asid%2Focoins.info%3Agenerator&rft.genre=article&rft_id=info%3Apmid%2F18025269">PMID:18025269</span> <ref name=PMID:18025269/> | ||
+ | |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]. | ||
+ | |tutorials=;[[MAKER Tutorial]] | ||
+ | :taught as part of the [[2013 GMOD Summer School]] | ||
+ | |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. | ||
+ | |req=* Perl 5.8.0 or higher | ||
+ | * [[BioPerl]] 1.6 or higher. | ||
+ | * [http://blast.wustl.edu WU-BLAST] 2.0 or higher or [http://www.ncbi.nlm.nih.gov/ NCBI-BLAST] 2.2.X or higher | ||
+ | * [http://www.repeatmasker.org/ RepeatMasker] 3.1.6 or higher | ||
+ | ** RepeatMasker requires a repeat library, available from [http://www.girinst.org/repbase/index.html Repbase]. | ||
+ | * [http://www.animalgenome.org/bioinfo/resources/manuals/exonerate/ Exonerate] 1.4 or higher. | ||
+ | |||
+ | Optional extras: | ||
+ | * [http://korflab.ucdavis.edu/software.html SNAP] version 2009-02-03 or higher (for eukaryotic genomes). | ||
+ | * [http://augustus.gobics.de Augustus] 2.0 or higher (for eukaryotic genomes) | ||
+ | * [http://exon.biology.gatech.edu GeneMark-ES] (for eukaryotic genomes) | ||
+ | * [http://www.softberry.com FGENESH] 2.6 or higher - requires licence (for eukaryotic genomes) | ||
+ | * [http://exon.biology.gatech.edu GeneMarkS] (for prokaryotic genomes) | ||
+ | |install=Please see the [http://www.yandell-lab.org/software/maker_install.html installation guide] or the README file in the download for instructions. | ||
+ | |config= | ||
+ | |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. | ||
+ | |||
+ | === 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 | ||
+ | |||
+ | |dev ppl=Yandell Lab, Utah; Ian Korf (University of California Davis) | ||
+ | |dev status= | ||
+ | |dl tracking= | ||
+ | |logo info= | ||
+ | |see also= | ||
+ | |extra= | ||
+ | }} | ||
+ | |||
+ | {{SemanticLink | ||
+ | |linkurl=http://www.yandell-lab.org/software/maker.html | ||
+ | |linktype=download | ||
+ | }} | ||
+ | |||
+ | {{SemanticLink | ||
+ | |linkurl=http://yandell.topaz.genetics.utah.edu/cgi-bin/maker_license.cgi | ||
+ | |linktype=source code | ||
+ | }} | ||
+ | |||
+ | {{SemanticLink | ||
+ | |linkurl=http://www.yandell-lab.org/software/maker.html | ||
+ | |linktype=website | ||
+ | }} | ||
+ | |||
+ | {{SemanticLink | ||
+ | |linkurl=http://derringer.genetics.utah.edu/cgi-bin/MWAS/maker.cgi | ||
+ | |linktype=public server | ||
+ | |linktitle=MAKER Web Annotation Server | ||
+ | |linkdesc=online version of the MAKER tool | ||
+ | }} | ||
+ | |||
+ | {{SemanticLink | ||
+ | |linkurl=http://hymenopteragenome.org/ant_genomes/ | ||
+ | |linktype=wild urls | ||
+ | |linktitle=Ant Genomes Portal | ||
+ | |linkdesc=The ant genomes were annotated using MAKER. | ||
+ | }} | ||
[[Category:GMOD Components]] | [[Category:GMOD Components]] | ||
[[Category:Annotation]] | [[Category:Annotation]] | ||
[[Category:MAKER]] | [[Category:MAKER]] |
Revision as of 22:13, 15 October 2013
Contents
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
Downloads
- MAKER is available as a compressed TAR file from the MAKER website.
- The source code for MAKER can be downloaded from http://yandell.topaz.genetics.utah.edu/cgi-bin/maker_license.cgi.
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
- Perl 5.8.0 or higher
- BioPerl 1.6 or higher.
- WU-BLAST 2.0 or higher or NCBI-BLAST 2.2.X or higher
- RepeatMasker 3.1.6 or higher
- RepeatMasker requires a repeat library, available from Repbase.
- Exonerate 1.4 or higher.
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
- MAKER—the easy-to-use genome annotation pipeline, presented by Mark Yandell at the SMBE 2009 GMOD Workshop.
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
- ↑ Cite error: Invalid
<ref>
tag; no text was provided for refs namedPMID:22192575
- ↑ Cite error: Invalid
<ref>
tag; no text was provided for refs namedPMID: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.
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 +, http://derringer.genetics.utah.edu/cgi-bin/MWAS/maker.cgi + and http://hymenopteragenome.org/ant_genomes/ + |
Has description | MAKER 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:
|
Has development status | active + |
Has download URL | http://yandell.topaz.genetics.utah.edu/cgi-bin/maker_license.cgi + |
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 | MAKER Web Annotation Server + and Ant Genomes Portal + |
Has topic | MAKER + |
Has website | http://www.yandell-lab.org/software/maker.html + |
Is open source | Caveats apply + |
Link type | download +, source code +, website + 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#http://derringer.genetics.utah.edu/cgi-bin/MWAS/maker.cgi + and MAKER#http://hymenopteragenome.org/ant_genomes/ + |