MAKER Has description
- MAKER is an easy-to-configure, portable ge … MAKER is an 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]]. 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
