Difference between revisions of "MAKER/tool data"

Revision as of 00:51, 12 December 2012

This page stores the data that populates the MAKER wiki page.

{{ {{{template}}} | name = MAKER | full_name = | status = mature | dev = active | support = active | type = | os_linux = | os_mac = y | os_unix = y | os_win = | os_web = | logo = MAKERLogo.png | home = http://www.yandell-lab.org/software/maker.html | about = 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.

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

| public_server = http://www.yandell-lab.org/software/mwas.html | dl = MAKER is available as a compressed TAR file from the MAKER website. | dl_url = http://www.yandell-lab.org/software/maker.html | dl_src = | dl_dev = | dl_src_url = | dl_dev_url = | 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.
• 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 extras:

• 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)

| install = An online installation guide is coming soon; please see 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 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

| papers = * MAKER: an easy-to-use annotation pipeline designed for emerging model organism genomes. PMID:18025269 ^[1] | presentations = * MAKER—the easy-to-use genome annotation pipeline, presented by Mark Yandell at the SMBE 2009 GMOD Workshop. | tutorials = * MAKER Tutorial | wild_urls = | mail =

Support for MAKER is provided on a mailing list, and through a Trac-based wiki, bug tracker and code browser. | logo_info = | dev_ppl = | dev_status = | contact_email = Mark Yandell | input = | output = | see_also = | demo_server = | survey_link = }}
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