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Method: Combining DNA and protein alignments to improve genome annotation with LiftOn
- Kuan-Hao Chao,
- Jakob M. Heinz,
- Celine Hoh,
- Alan Mao,
- Alaina Shumate,
- Mihaela Pertea,
- and Steven L. Salzberg
Genome Res. February 2025 35: 311-325; Published in Advance December 27, 2024, doi:10.1101/gr.279620.124
...'Leary et al. 2016; Frankish et al. 2019; Salzberg 2019). The most widely used approaches to annotation are software pipelines such as MAKER, MAKER-P (Cantarel et al. 2008; Campbell et al. 2014), BRAKER, and BRAKER2 (Hoff et al. 2019; Brůna et al. 2021), which combine ab initio prediction, protein...
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Method: Identifying genes within pathways in unannotated genomes with PaGeSearch
- Sohyoung Won,
- Jaewoong Yu,
- and Heebal Kim
Genome Res. May 2024 34: 784-795; Published in Advance June 10, 2024, doi:10.1101/gr.278566.123
..., Xie C, Huson DH. 2015. Fast and sensitive protein alignment using DIAMOND. Nat Methods 12: 59–60. doi:10.1038/nmeth.3176 ↵Cantarel BL, Korf I, Robb SM, Parra G, Ross E, Moore B, Holt C, Alvarado AS, Yandell M. 2008. MAKER: an easy-to-use annotation pipeline designed for emerging model organism s...
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Method: Comparative Annotation Toolkit (CAT)—simultaneous clade and personal genome annotation
- Ian T. Fiddes,
- Joel Armstrong,
- Mark Diekhans,
- Stefanie Nachtweide,
- Zev N. Kronenberg,
- Jason G. Underwood,
- David Gordon,
- Dent Earl,
- Thomas Keane,
- Evan E. Eichler,
- David Haussler,
- Mario Stanke,
- and Benedict Paten
Genome Res. July 2018 28: 1029-1038; Published in Advance June 8, 2018, doi:10.1101/gr.233460.117
..., Robb SM, Parra G, Ross E, Moore B, Holt C, Alvarado AS, Yandell M. 2008. Maker: an easy-to-use annotation pipeline designed for emerging model organism s. Genome Res 18: 188–196. ↵Chaisson MJ, Wilson RK, Eichler EE. 2015. Genetic variation and the de novo assembly of human s. Nat Rev Genet 16: 627...
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Research: Pangolin genomes and the evolution of mammalian scales and immunity
- Siew Woh Choo,
- Mike Rayko,
- Tze King Tan,
- Ranjeev Hari,
- Aleksey Komissarov,
- Wei Yee Wee,
- Andrey A. Yurchenko,
- Sergey Kliver,
- Gaik Tamazian,
- Agostinho Antunes,
- Richard K. Wilson,
- Wesley C. Warren,
- Klaus-Peter Koepfli,
- Patrick Minx,
- Ksenia Krasheninnikova,
- Antoinette Kotze,
- Desire L. Dalton,
- Elaine Vermaak,
- Ian C. Paterson,
- Pavel Dobrynin,
- Frankie Thomas Sitam,
- Jeffrine J. Rovie-Ryan,
- Warren E. Johnson,
- Aini Mohamed Yusoff,
- Shu-Jin Luo,
- Kayal Vizi Karuppannan,
- Gang Fang,
- Deyou Zheng,
- Mark B. Gerstein,
- Leonard Lipovich,
- Stephen J. O'Brien,
- and Guat Jah Wong
Genome Res. October 2016 26: 1312-1322; Published in Advance August 10, 2016, doi:10.1101/gr.203521.115
...-Emonds OR, Cardillo M, Jones KE, MacPhee RD, Beck RM, Grenyer R, Price SA, Vos RA, Gittleman JL, Purvis A. 2007. The delayed rise of present-day mammals. Nature 446: 507–512. Cantarel BL, Korf I, Robb SM, Parra G, Ross E, Moore B, Holt C, Sanchez Alvarado A, Yandell M. 2008. MAKER: an easy-to-use annotation...
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Resource: Building better genome annotations across the tree of life
- Adam H. Freedman and
- Timothy B. Sackton
Genome Res. May 2025 35: 1261-1276; Published in Advance April 15, 2025, doi:10.1101/gr.280377.124
...from the three major approaches to the annotation problem. At the core of six of these—MAKER (Cantarel et al. 2008) with both protein and RNA-seq evidence; BRAKER1 (RNA-seq evidence only); BRAKER2 (protein evidence only); BRAKER3 (protein and RNA-seq evidence); CGP using protein evidence; and CGP...
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Resource: Long-read assembly and comparative evidence-based reanalysis of Cryptosporidium genome sequences reveal expanded transporter repertoire and duplication of entire chromosome ends including subtelomeric regions
- Rodrigo P. Baptista,
- Yiran Li,
- Adam Sateriale,
- Mandy J. Sanders,
- Karen L. Brooks,
- Alan Tracey,
- Brendan R.E. Ansell,
- Aaron R. Jex,
- Garrett W. Cooper,
- Ethan D. Smith,
- Rui Xiao,
- Jennifer E. Dumaine,
- Peter Georgeson,
- Bernard J. Pope,
- Matthew Berriman,
- Boris Striepen,
- James A. Cotton,
- and Jessica C. Kissinger
Genome Res. January 2022 32: 203-213; Published in Advance November 11, 2021, doi:10.1101/gr.275325.121
..., Ross E, Moore B, Holt C, Sanchez Alvarado A, Yandell M. 2008. MAKER: an easy-to-use annotation pipeline designed for emerging model organism s. Genome Res 18: 188–196. doi:10.1101/gr.6743907 ↵Carver TJ, Rutherford KM, Berriman M, Rajandream MA, Barrell BG, Parkhill J. 2005. ACT: the Artemis comparison...
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Resource: A new emu genome illuminates the evolution of genome configuration and nuclear architecture of avian chromosomes
- Jing Liu,
- Zongji Wang,
- Jing Li,
- Luohao Xu,
- Jiaqi Liu,
- Shaohong Feng,
- Chunxue Guo,
- Shengchan Chen,
- Zhanjun Ren,
- Jinpeng Rao,
- Kai Wei,
- Yuezhou Chen,
- Erich D. Jarvis,
- Guojie Zhang,
- and Qi Zhou
Genome Res. March 2021 31: 497-511; Published in Advance January 6, 2021, doi:10.1101/gr.271569.120
...-generation long-read sequencing and Hi-C technologies with the pipeline of the Vertebrate Genomes Project (Rhie et al. 2020). By comparing the new emu to other chromosome-level assemblies of 11 bird and one turtle species, we estimated the tempo of inter- and intrachromosomal rearrangements in major lineages...
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Resource: De novo assembly and validation of planaria transcriptome by massive parallel sequencing and shotgun proteomics
- Catherine Adamidi,
- Yongbo Wang,
- Dominic Gruen,
- Guido Mastrobuoni,
- Xintian You,
- Dominic Tolle,
- Matthias Dodt,
- Sebastian D. Mackowiak,
- Andreas Gogol-Doering,
- Pinar Oenal,
- Agnieszka Rybak,
- Eric Ross,
- Alejandro Sánchez Alvarado,
- Stefan Kempa,
- Christoph Dieterich,
- Nikolaus Rajewsky,
- and Wei Chen
Genome Res. July 2011 21: 1193-1200; Published in Advance May 2, 2011, doi:10.1101/gr.113779.110
.... Bioinformatics 22: e9–e15. Cantarel BL, Korf I, Robb SMC, Parra G, Ross E, Moore B, Holt C, Sa´nchez Alvarado A, Yandell M. 2008. MAKER: An easy-to-use annotation pipeline designed for emerging model organism s. Genome Res 18: 188–196. Cox J, Mann M. 2008. MaxQuant enables high peptide identification rates...
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RESOURCE: eShadow: A Tool for Comparing Closely Related Sequences
- Ivan Ovcharenko,
- Dario Boffelli,
- and Gabriela G. Loots
Genome Res. June 2004 14: 1191-1198; doi:10.1101/gr.1773104
...://www.ensembl.org/ ; Ensembl. http://eshadow.dcode.org/ ; eShadow. http://.ucsc.edu/ ; Human Genome Browser at UCSC. http://bio.cse.psu.edu//hummus/ ; Pip Dispenser. http://bio.cse.psu.edu/pipmaker/ ; PipMaker. http://www.sanger.ac.uk/Software/Pfam/ ; Pfam database. http://www-gsd.lbl.gov/VISTA/ ; Vista. http://pipeline...
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Research: Transposon wave remodeled the epigenomic landscape in the rapid evolution of X-Chromosome dosage compensation
- David C.H. Metzger,
- Imogen Porter,
- Brendan Mobley,
- Benjamin A. Sandkam,
- Lydia J.M. Fong,
- Andrew P. Anderson,
- and Judith E. Mank
Genome Res. November 2023 33: 1917-1931; Published in Advance November 21, 2023, doi:10.1101/gr.278127.123
...landscape and the rapid de novo origin of a dosage compensation system.Complete dosage compensation mechanisms have evolved in some organisms with highly diverged sex chromosomes to ameliorate the negative effects of haploinsuffiency (Ohno 1967; Bachtrog 2013). These complex mechanisms act across...

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