MAKER protocols

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MAKER specifications

Information


Unique identifier OMICS_13535
Name MAKER
Alternative name MAKER2
Interface Web user interface
Restrictions to use Academic or non-commercial use
Input data Genome sequences, annotations
Input format FASTA, GFF3
License Artistic License version 2.0, GNU General Public License version 3.0
Computer skills Basic
Version 1.0
Stability Stable
Maintained Yes

Documentation


Maintainer


  • person_outline Mark Yandell <>

Information


Unique identifier OMICS_13535
Name MAKER
Alternative name MAKER2
Software type Pipeline/Workflow
Interface Graphical user interface
Restrictions to use Academic or non-commercial use
Input data Genome sequences, annotations
Input format FASTA, GFF3
Operating system Unix/Linux, Mac OS
Programming languages Perl
License Artistic License version 2.0, GNU General Public License version 3.0
Computer skills Medium
Version 2.31.8
Stability Stable
Requirements
SNAP, RepeatMasker, Exonerate, NCBI BLAST
Maintained Yes

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Documentation


Maintainer


  • person_outline Mark Yandell <>

Publication for MAKER

MAKER in pipelines

 (16)
2018
PMCID: 5882950
PMID: 29615780
DOI: 10.1038/s41598-018-23749-w

[…] our assembly. overall, these results indicate that the b. leachii de novo genome assembly was largely complete and suitable for annotation.table 2, ab initio genome annotation was performed using maker2 and predicted 15,839 coding genes, of which 13,507 could be classified using interproscan. comparing these predictions with our mapping of the transcriptome, we found out that 83% […]

2018
PMCID: 5924542
PMID: 29642531
DOI: 10.3390/genes9040200

[…] we confirmed them with at least one gene hit using reciprocal blast searches. divergent homologs were shown as outgroups of annotated genes. rna-seq reads were mapped to the assembled genome []. maker2 was used to tune-up the annotation and modeling []., molecular phylogenic analyses of phytoene desaturase (crti), geranylgeranyl phytoene synthase (crtb), and geranylgeranyl phytoene synthase […]

2017
PMCID: 5591544
PMID: 28886750
DOI: 10.1186/s13062-017-0191-4

[…] identity cutoff of >90%. predictions that have both nr plant refseq and e. guineensis mrna support were selected for further analysis., seqping [], a customized gene prediction pipeline based on maker2 [], was developed by mpob. full-length open reading frames (orfs) were identified from the e. guineensis mrna dataset described above, using the emboss getorf program. orfs between 500 […]

2017
PMCID: 5679801
PMID: 29122868
DOI: 10.1128/genomeA.01209-17

[…] scaffold size of 7,305,194 bp. the completeness of the assembly was assessed using busco v12 (), which estimated the genome sequence to be 99.86% complete. the nuclear genome was annotated using the maker2 pipeline (). overall, 11,827 protein-coding gene models were predicted. analysis with signalp 4.1 () revealed that 1,288 predicted proteins (10.9% of the proteome) contain a secretion signal […]

2017
PMCID: 5824900
PMID: 29036429
DOI: 10.1093/dnares/dsx038

[…] isoforms of multiexon genes, small rnas, and lncrnas. an optimized workflow to annotate protein-coding genes and their isoforms is shown in . to take advantage of the extensive rna-seq datasets, maker2, specifically designed for second-generation genome projects, was first used to generate an initial protein-coding gene annotation. input data for maker2 include (i) repeats masked genome fvb, […]


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MAKER in publications

 (117)
PMCID: 5931083
PMID: 29718005
DOI: 10.1038/sdata.2018.79

[…] simplify the subsequent analyses, only those transcripts with the longest open reading frame (orf) were selected as representatives. protein-coding genes on the novel sequences were predicted using maker2 (a gene prediction pipeline combining ab initio predictions, expression evidence and protein homologies). in detail, low-complexity repeats were first masked. two ab initio predictors, snap […]

PMCID: 5920178
PMID: 29700153
DOI: 10.1128/genomeA.00321-18

[…] in 9 chromosomes (1 mitochondrial chromosome) and an average gc content of 42%. the genome was first annotated with ygap (), and 5,231 genes were predicted. an improved annotation was performed with maker2 (), providing star rna alignment information () for the prediction of protein-coding genes. a total of 4,831 protein-coding genes were identified, compared to 4,714 and 4,972 protein-coding […]

PMCID: 5916904
PMID: 29695739
DOI: 10.1038/s41598-018-24939-2

[…] te protein database. for de novo prediction, repeatmodeler (http://repeatmasker.org/) and ltr finder were used to identify de novo evolved repeats inferred from the assembled genome., we used the maker2 pipeline to predict protein-coding genes in the genome. first, the genome was repeat masked using the result of repeat annotation. then the masked genome was fed to the maker2 pipeline […]

PMCID: 5915685
PMID: 29689067
DOI: 10.1371/journal.pone.0196303

[…] with a combination of repeatmasker version 4.0.5 and repeatmodeler version 1.0.8. to predict gene structures, augustus version 3.1 [], snap version 2013-11-29 [], genemark-es version 2.3c [], and maker2 version 2.31.8 [] were used in combination. augustus and snap were trained with gene models of the jgi glomerella cingulate 23 strain (http://genome.jgi.doe.gov/programs/fungi/index.jsf), […]

PMCID: 5907747
PMID: 29673315
DOI: 10.1186/s12864-018-4612-2

[…] to f. venenatum vs f. graminearum where a blastp hit was found in f. oxysporum. the gc content was 47.6%, which is comparable to 48% for f. graminearum []. gene modelling was performed using maker2 [], yielding 13,946 genes. average gene coding length in f. venenatum and f. graminearum was respectively 1388 vs. 1372 bp, with 2.78 vs. 2.76 exons per gene (average exon and intron length […]


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MAKER institution(s)
Eccles Institute of Human Genetics, University of Utah, Salt Lake City, UT, USA; Ontario Institute for Cancer Research, MaRS Centre, ON, Canada
MAKER funding source(s)
This work was supported by the grants NIH/NHGRI-R01-HG004694 and NSF IOS-1126998 and partially supported by the NIH Genetics Training Grant T32-GM007464.

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