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Difference between revisions of "MAKER"
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| − | MAKER is a portable and easy to configure genome [[:Category:Annotation|annotation]] pipeline. It's purpose is to allow smaller ''eukaryotic'' 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]], and [[Apollo]]. | + | MAKER is a portable and easy to configure genome [[:Category:Annotation|annotation]] pipeline. It's purpose is to allow smaller ''eukaryotic'' genome projects and (with the most recent version) ''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]], and [[Apollo]]. |
| − | Note | + | Note MAKER is designed to handle the idiosyncrasies of eukaryotic genomes. If you wish to annotate prokaryotic genomes please [[#Contact|contact]] the Yandell lab for other options. |
== Annotations == | == Annotations == | ||
Revision as of 16:30, 21 August 2009
__NOTITLE__ MAKER is a portable and easy to configure genome annotation pipeline. It's purpose is to allow smaller eukaryotic genome projects and (with the most recent version) 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 FASTA format, and can be directly loaded into Chado, GBrowse, and Apollo.
Note MAKER is designed to handle the idiosyncrasies of eukaryotic genomes. If you wish to annotate prokaryotic genomes please contact the Yandell lab for other options.
Contents
Annotations
The MAKER genome annotation pipeline generates several different types of annotations, including
|
File:MAKERAnnotations500x301.jpg |
| MAKER generated annotations, shown in Apollo. |
Requirements
- Perl 5.8.0 or higher
- BioPerl 1.5 or higher.
- WU-BLAST 2.0
- SNAP version 2008-04-10. Also works with version 2006-07-28.
- RepeatMasker 3.1.6
- RepeatMasker requires a repeat library, available from Repbase.
- Exonerate 1.4. MAKER also appears to work with Exonerate 2.0, but this has not yet been thoroughly tested.
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.)
Documentation
MAKER documentation is available from these sources:
- 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. (requires subscription)
- README file in the download
Read both the paper and the README before installing MAKER.
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 at http://www.yandell-lab.org/software/maker.html.
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>
