Difference between revisions of "MAKER"

Revision as of 07:00, 28 June 2012 (view source) Clements (Talk | contribs) ← Older edit		Revision as of 18:15, 12 July 2012 (view source) Girlwithglasses (Talk | contribs) m (Couple of grammar fixes, corrected a link) Newer edit →
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	{{ComponentBox|{{MAKERResourcesBoxItem}}|{{ComponentBoxEventsHeader}}|{{SchoolBoxItem|MAKER}} | | | |}}		{{ComponentBox|{{MAKERResourcesBoxItem}}|{{ComponentBoxEventsHeader}}|{{SchoolBoxItem|MAKER}} | | | |}}
−	MAKER is a portable and easy to configure genome [[:Category:Annotation|annotation]] pipeline. It's purpose is to allow smaller ''eukaryotic'' genome projects and (as of August 2009) ''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 having 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.  It outputs are in [[GFF3]] or [[Glossary#FASTA|FASTA]] format, and can be directly loaded into [[Chado]], [[GBrowse]], [[JBrowse]] or [[Apollo]].	+	MAKER is a portable and easy to configure genome [[:Category:Annotation|annotation]] pipeline. MAKER allows smaller ''eukaryotic'' genome projects and (as of August 2009) ''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]] or [[Apollo]].
	Additional MAKER options/capabilities include:		Additional MAKER options/capabilities include:
−	* Map old annotation sets onto new assemblies.	+	* Map old annotation sets on to new assemblies.
	* Merge multiple legacy annotation sets into a consensus set of annotations.		* Merge multiple legacy annotation sets into a consensus set of annotations.
	* Update existing annotations to take new evidence into account.		* Update existing annotations to take new evidence into account.
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	* Use GFF3 pass-through to include both evidence alignments and predicted gene models from algorithms not natively supported by MAKER.		* 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.		* 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]], [[GBrowse]], or [[Apollo]].	+	* 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]].
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	* <tt>README</tt> file in the download		* <tt>README</tt> file in the download
−	Read both the paper and the <tt>README</tt> before installing <tt>MAKER</tt>.	+	Read both the paper and the <tt>README</tt> before installing MAKER.
	== Annotations ==		== Annotations ==
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	== Downloads ==		== Downloads ==
−	A compressed TAR file is available at http://www.yandell-lab.org/software/maker.html.	+	A compressed TAR file is available from the [http://www.yandell-lab.org/software/maker.html MAKER website].
	== Demo ==		== Demo ==

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Revision as of 18:15, 12 July 2012

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Status

• Mature release
• Active development
• Active support

Resources

• Home Page
• Tutorial
• MWAS
• Mailing List
• 2008 SurveyTemplate:ComponentBoxEventsHeader

MAKER is a portable and easy to configure genome annotation pipeline. MAKER allows smaller eukaryotic genome projects and (as of August 2009) 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.

Documentation

MAKER documentation is available from these sources:

• MAKER Tutorial
• MAKER: An easy-to-use annotation pipeline designed for emerging model organism genomes, by Brandi L. Cantarel, Ian Korf, Sofia M.C. Robb, Genis Parra, Eric Ross, Barry Moore, Carson Holt, Alejandro, Sánchez Alvarado and Mark Yandell. 2008 18: 188-196; Genome Res.
• README file in the download

Read both the paper and the README before installing MAKER.

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

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
• SNAP version 2009-02-03 or higher (for eukaryotic genomes).
• RepeatMasker 3.1.6 or higher
  • RepeatMasker requires a repeat library, available from Repbase.
• Exonerate 1.4 or higher.

Optional Components

• 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)

mpi_maker

MAKER, by default runs on a single computer. A parallel version, mpi_maker, is also available. To run mpi_maker you will need an MPI package installed on all participating computers. Try MPICH2. Remember to install MPICH2 with the --enable-sharedlibs flag set to the appropriate value (See theMPICH2 Installer's Guide.)

Presentations

• MAKER—the easy-to-use genome annotation pipeline, presented by Mark Yandell at the SMBE 2009 GMOD Workshop.

Downloads

A compressed TAR file is available from the MAKER website.

Demo

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

Since MAKER is a command driven pipeline there are no screenshots or online demos available.

Support

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

Contact

Mark Yandell <myandell@genetics.utah.edu>