MAKER statistics

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Citations per year

Number of citations per year for the bioinformatics software tool MAKER
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Tool usage distribution map

This map represents all the scientific publications referring to MAKER per scientific context
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Protocols

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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Versioning


No version available

Documentation


Maintainer


  • person_outline Mark Yandell

Publication for MAKER

MAKER citations

 (114)
library_books

Novel sequences, structural variations and gene presence variations of Asian cultivated rice

2018
Sci Data
PMCID: 5931083
PMID: 29718005
DOI: 10.1038/sdata.2018.79

[…] o 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 and […]

library_books

Genome Sequence of Australian Indigenous Wine Yeast Torulaspora delbrueckii COFT1 Using Nanopore Sequencing

2018
Genome Announc
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 gen […]

library_books

The Phytophthora cactorum genome provides insights into the adaptation to host defense compounds and fungicides

2018
Sci Rep
PMCID: 5916904
PMID: 29695739
DOI: 10.1038/s41598-018-24939-2

[…] 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 with the […]

library_books

Pathogenic adaptations of Colletotrichum fungi revealed by genome wide gene family evolutionary analyses

2018
PLoS One
PMCID: 5915685
PMID: 29689067
DOI: 10.1371/journal.pone.0196303

[…] strain (http://genome.jgi.doe.gov/programs/fungi/index.jsf), GeneMark-ES was self-trained. Prediction results of Augustus, GeneMark-ES, and protein models of G. cingulate 23 were combined for a final MAKER2 integration. Predicted genes were functionally annotated with the Blast2GO software [], putative functions were assigned based on BLASTP search against a local NCBI nr database (release date: 2 […]

library_books

Inter genome comparison of the Quorn fungus Fusarium venenatum and the closely related plant infecting pathogen Fusarium graminearum

2018
BMC Genomics
PMCID: 5907747
PMID: 29673315
DOI: 10.1186/s12864-018-4612-2

[…] specific 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 500 […]

library_books

Genome wide analysis of the transition to pathogenic lifestyles in Magnaporthales fungi

2018
Sci Rep
PMCID: 5897359
PMID: 29651164
DOI: 10.1038/s41598-018-24301-6

[…] R2 package with three gene prediction tools used: AUGUSTUS,, SNAP and the ab initio tool GeneMark-ES version 2. AUGUSTUS was trained with M. oryzae, and SNAP was initially trained with CEGMA results. MAKER2 was run for four iterations for each genome. Gene models from the previous run were used for re-training in the following run. Adapter-trimmed transcriptome sequences were used to assemble EST […]


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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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