MAKER-P protocols

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MAKER-P specifications

Information


Unique identifier OMICS_04638
Name MAKER-P
Software type Pipeline/Workflow
Interface Command line interface
Restrictions to use Academic or non-commercial use
Operating system Unix/Linux
License Artistic License version 2.0, GNU General Public License version 2.0
Computer skills Advanced
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Mark Yandell <>

Publication for MAKER-P

MAKER-P in pipelines

 (2)
2016
PMCID: 5381527
PMID: 28173009
DOI: 10.1093/gbe/evw253

[…] per side (a), indicating that a duplicated sequence in two different locations. in the same way, we obtained a better resolution on the rymv1 locus () than on the omap reference (b). fig. 1.—, the maker-p structural annotation provided between 49,000 and 51,262 gene locations per assembly (), with more than 160,000 models (mean 3.2 mrna possibilities per gene location) per assembly, […]

2014
PMCID: 4268812
PMID: 25468217
DOI: 10.1186/s13059-014-0506-z

[…] interproscan 5 software [], available within the iplant discovery environment []. among resulting interpro domains we curated 21 as being associated with transposon-encoded genes and screened out maker-p annotations with these domains (ipr000477, ipr001207, ipr001584, ipr002559, ipr004242, ipr004252, ipr004264, ipr004330, ipr004332, ipr005063, ipr005162, ipr006912, ipr007321, ipr013103, […]


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MAKER-P in publications

 (23)
PMCID: 5960304
PMID: 29717040
DOI: 10.1073/pnas.1721395115

[…] mapped back to the assemblies (si appendix, table s4), and 94–98% of cegma () and busco () genes were detected (si appendix, table s5)., repetitive elements were identified following the standard maker-p recipe (weatherby.genetics.utah.edu/maker/wiki/index.php/repeat_library_construction-advanced, accessed october 2015) as described on the gmod site: (i) repeatmodeler with repeatscout v1.0.5, […]

PMCID: 5801600
PMID: 29253147
DOI: 10.1093/gigascience/gix124

[…] volume of transcript and protein sequence information generated from various experimental studies, the task of improving genome annotation of such genomes remains a major challenge. using the maker-p annotation pipeline (maker, rrid:scr_005309) [], publicly available transcriptome data of f. vesca, and protein sequences from arabidopsis thaliana and the uniprotkb database as evidence, […]

PMCID: 5723288
PMID: 29259619
DOI: 10.3389/fgene.2017.00180

[…] of satsuma constructed by aligning the scaffolds to three genetic maps showed genome-wide synteny to the genomes of clementine, pummelo, and sweet orange. gene prediction by modeling with maker-p proposed 29,024 genes and 37,970 mrna; additionally, gene prediction analysis found candidates for novel genes in several biosynthesis pathways for gibberellin and violaxanthin catabolism. […]

PMCID: 5710592
PMID: 29048480
DOI: 10.1093/gigascience/gix093

[…] against the te protein database. the tandem repeats in the genome assembly were identified through the tandem repeat finder., the gene models of the p. ginseng genome were predicted using the maker-p pipeline []. the available ginseng est, mrna datasets, and protein datasets were used to generate the first-pass gene annotation. the resulting gff3 file was used for ab initio gene predictor […]

PMCID: 5591544
PMID: 28886750
DOI: 10.1186/s13062-017-0191-4

[…] using mega6 [] and mafft []. all programs were used with their default settings., a variety of tools has been developed for prediction and annotation of protein-coding genes, such as fgenesh++ [], maker-p [], gramene [], genemark [, ], and ensembl []. plant genomes (such as a. thaliana, medicago truncatula, o. sativa, e. guineensis, fragaria vesca and others) are generally annotated using […]


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MAKER-P institution(s)
Eccles Institute of Human Genetics, University of Utah, Salt Lake City, Utah

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