MAKER Has description
- MAKER is an easy-to-configure, portable
ge …
MAKER is an easy-to-configure,
portable genome [[:Category%253AAnnotation|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]]. For those annotating novel plant
genomes, the [http://www.yandell-lab.org/software/maker-p.html
MAKER-P pipeline] is designed to make the annotation tractable for
small groups with limited bioinformatics experience and resources, and
faster and more transparent for large groups with more experience and
resources. The MAKER-P pipeline generates species-specific repeat
libraries, as well as structural annotations of protein coding genes,
non-coding RNAs, and pseudogenes. The
[http://www.yandell-lab.org/software/maker-p.html MAKER-P website]
has more information on the additional protocols for plant genome
annotation. 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.data</tt> directory in the download.
- MAKER with additional software for plant genome annotation
- Review article on eukaryotic genome annotation from the MAKER team.
- The ant genomes were annotated using MAKER.
- online version of the MAKER tool
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