MAKER: an easy-to-use annotation pipeline designed for emerging model organism genomes.
By Brandi L. Cantarel, Ian Korf, Sofia M. C. Robb, Genís Parra, E. Ross, Barry Moore, Carson Holt, A. Sánchez Alvarado, Mark Yandell. Genome Research, 2007
1,869 citations recorded by the source corpus.
Subfields: Genetics, Global and Planetary Change, Molecular Biology
View Paper: https://www.semanticscholar.org/paper/cce55765c668c28548b2b64d8dd9a3757e402bec
How researchers see this paper
The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.
In Genetics
- Edith Gourbeyre
- Michael Campbell
- Barry Moore
- Mark Yandell
- Carson Holt
- Patricia Siguier
- Michael Chandler
- Yingjie Zhu
In Molecular Biology
- Edith Gourbeyre
- Barry Moore
- Michael Campbell
- Carson Holt
- Mark Yandell
- Patricia Siguier
- Michael Chandler
- Yingjie Zhu
Citations in the corpus
- ISsaga is an ensemble of web-based methods for high throughput identification and semi-automatic annotation of insertion sequences in prokaryotic genomes (2011, background): “Unfortunately, expert genome annotation is fast becoming a bottleneck in genomics [2].”
- MAKER2: an annotation pipeline and genome-database management tool for second-generation genome projects (2011, neutral): “humile [6,9], both values well below the 63,622 and 420,224 gene predictions produced (respectively) when running SNAP on its own (outside of MAKER2).”
- BRAKER2: automatic eukaryotic genome annotation with GeneMark-EP+ and AUGUSTUS supported by a protein database (2020, neutral): “…metrics are less precise in assessment of accuracy of gene prediction than the methods comparing coordinates of predicted and annotated genes and computing Sn, Sp and F1 values. such as ab initio gene predictions, mapped RNA-seq reads as well as alignments of proteins to the genome (33,40,41).”
- CpGAVAS, an integrated web server for the annotation, visualization, analysis, and GenBank submission of completely sequenced chloroplast genome sequences (2012, methodology): “Our pipeline is actually similar to part of the Maker pipeline in terms of determining the gene structures.”
- Genome Annotation and Curation Using MAKER and MAKER-P (2014, methodology): “Since it starts with maker , we know that that it is derived from a MAKER ‘hint-based’ prediction (for more information about how MAKER passes evidence derived ‘hints’ to the gene predictors, see Cantarel et al., 2008; Holt and Yandell, 2011).”