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Method: Leveraging protein language models for accurate multiple sequence alignments
- Claire D. McWhite,
- Isabel Armour-Garb,
- and Mona Singh
Genome Res. July 2023 33: 1145-1153; Published in Advance July 6, 2023, doi:10.1101/gr.277675.123
.... Sci Rep 6: 33964. doi:10.1038/srep33964 ↵Do CB, Mahabhashyam MSP, Brudno M, Batzoglou S. 2005. ProbCons: probabilistic consistency-based multiple sequence alignment. Genome Res 15: 330–340. doi:10.1101/gr.2821705 ↵Eades P, Lin X, Smyth WF. 1993. A fast and effective heuristic for the feedback arc set...
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Methods: Uncertainty in homology inferences: Assessing and improving genomic sequence alignment
- Gerton Lunter,
- Andrea Rocco,
- Naila Mimouni,
- Andreas Heger,
- Alexandre Caldeira,
- and Jotun Hein
Genome Res. February 2008 18: 298-309; Published in Advance December 11, 2007, doi:10.1101/gr.6725608
...of inferring nucleotide-level homology. We also do not consider the multiple-alignment problem, which is essentially more difficult than pairwise alignments. However, a detailed understanding of the issues concerning pairwise alignments will, we hope, help guide the design of probabilistic multiple-alignment...
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Resource: Multiple whole-genome alignments without a reference organism
- Inna Dubchak,
- Alexander Poliakov,
- Andrey Kislyuk,
- and Michael Brudno
Genome Res. April 2009 19: 682-689; Published in Advance January 28, 2009, doi:10.1101/gr.081778.108
.... 2004. Accurate identification of novel human genes through simultaneous gene prediction in human, mouse, and rat. Genome Res. 14: 661–664. Do, C.B., Mahabhashyam, M.S., Brudno, M., and Batzoglou, S. 2005. ProbCons: Probabilistic consistency-based multiple sequence alignment. Genome Res. 15: 330...
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Research: High sensitivity to aligner and high rate of false positives in the estimates of positive selection in the 12 Drosophila genomes
- Penka Markova-Raina and
- Dmitri Petrov
Genome Res. June 2011 21: 863-874; Published in Advance March 10, 2011, doi:10.1101/gr.115949.110
...-coding genes in 12 Drosophila genomes annotated in either all 12 species (∼6690 genes) or in the six melanogaster group species. We compare six popular aligners: PRANK, T-Coffee, ClustalW, ProbCons, AMAP, and MUSCLE, and find that the aligner choice strongly influences the estimates of positive selection...
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Methods: Genome-wide nucleotide-level mammalian ancestor reconstruction
- Benedict Paten,
- Javier Herrero,
- Stephen Fitzgerald,
- Kathryn Beal,
- Paul Flicek,
- Ian Holmes,
- and Ewan Birney
Genome Res. November 2008 18: 1829-1843; Published in Advance October 10, 2008, doi:10.1101/gr.076521.108
...that have driven evolution. We present a new evolutionary alignment modeler, called “Ortheus,” for inferring the evolutionary history of a multiple alignment, in terms of both substitutions and, importantly, insertions and deletions. Based on a multiple sequence probabilistic transducer model of the type...
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ARTICLE: Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome
- Elliott H. Margulies,
- Gregory M. Cooper,
- George Asimenos,
- Daryl J. Thomas,
- Colin N. Dewey,
- Adam Siepel,
- Ewan Birney,
- Damian Keefe,
- Ariel S. Schwartz,
- Minmei Hou,
- James Taylor,
- Sergey Nikolaev,
- Juan I. Montoya-Burgos,
- Ari Löytynoja,
- Simon Whelan,
- Fabio Pardi,
- Tim Massingham,
- James B. Brown,
- Peter Bickel,
- Ian Holmes,
- James C. Mullikin,
- Abel Ureta-Vidal,
- Benedict Paten,
- Eric A. Stone,
- Kate R. Rosenbloom,
- W. James Kent,
- Gerard G. Bouffard,
- Xiaobin Guan,
- Nancy F. Hansen,
- Jacquelyn R. Idol,
- Valerie V.B. Maduro,
- Baishali Maskeri,
- Jennifer C. McDowell,
- Morgan Park,
- Pamela J. Thomas,
- Alice C. Young,
- Robert W. Blakesley,
- Donna M. Muzny,
- Erica Sodergren,
- David A. Wheeler,
- Kim C. Worley,
- Huaiyang Jiang,
- George M. Weinstock,
- Richard A. Gibbs,
- Tina Graves,
- Robert Fulton,
- Elaine R. Mardis,
- Richard K. Wilson,
- Michele Clamp,
- James Cuff,
- Sante Gnerre,
- David B. Jaffe,
- Jean L. Chang,
- Kerstin Lindblad-Toh,
- Eric S. Lander,
- Angie Hinrichs,
- Heather Trumbower,
- Hiram Clawson,
- Ann Zweig,
- Robert M. Kuhn,
- Galt Barber,
- Rachel Harte,
- Donna Karolchik,
- Matthew A. Field,
- Richard A. Moore,
- Carrie A. Matthewson,
- Jacqueline E. Schein,
- Marco A. Marra,
- Stylianos E. Antonarakis,
- Serafim Batzoglou,
- Nick Goldman,
- Ross Hardison,
- David Haussler,
- Webb Miller,
- Lior Pachter,
- Eric D. Green,
- and Arend Sidow
Genome Res. June 2007 17: 760-774; doi:10.1101/gr.6034307
...the alignments and constraint-detecting methods, we produced constraint annotations that were found to be robust based on multiple independent measures. Analyses of these annotations illustrate that most classes of experimentally annotated functional elements are enriched for constrained sequences; however...
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Resource: ProPhylER: A curated online resource for protein function and structure based on evolutionary constraint analyses
- Jonathan Binkley,
- Kalpana Karra,
- Andrew Kirby,
- Midori Hosobuchi,
- Eric A. Stone,
- and Arend Sidow
Genome Res. January 2010 20: 142-154; Published in Advance October 21, 2009, doi:10.1101/gr.097121.109
...originating earlier in evolution are carried by a larger number of species, and are thus better represented in the sequence databases. Sensitivity of ProPhylER’s constraint analyses depends on the quality of the multiple alignments of cluster sequences. The alignment program ProbCons produces a reliability...
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LETTER: Network-level molecular evolutionary analysis of the insulin/TOR signal transduction pathway across 12 Drosophila genomes
- David Alvarez-Ponce,
- Montserrat Aguadé,
- and Julio Rozas
Genome Res. February 2009 19: 234-242; Published in Advance January 13, 2009, doi:10.1101/gr.084038.108
...of a kinase with multiple roles in mitogenic signalling . Curr. Opin. Cell Biol. 7 : 806 – 814 . ↵ Do, C.B. , Mahabhashyam, M.S. , Brudno, M. , Batzoglou, S. ( 2005 ) ProbCons: Probabilistic consistency-based multiple sequence alignment . Genome Res. 15 : 330 – 340 . ↵ Dong, J. , Pan, D. ( 2004 ) Tsc2...
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LETTER: A highly divergent gene cluster in honey bees encodes a novel silk family
- Tara D. Sutherland,
- Peter M. Campbell,
- Sarah Weisman,
- Holly E. Trueman,
- Alagacone Sriskantha,
- Wolfgang J. Wanjura,
- and Victoria S. Haritos
Genome Res. November 2006 16: 1414-1421; Published in Advance October 25, 2006, doi:10.1101/gr.5052606
...: Probabilistic consistency-based multiple sequence alignment . Genome Res. 15 : 330 – 340 . ↵ Edgar, R.C. ( 2004 ) MUSCLE: Multiple sequence alignment with high accuracy and high throughput . Nucleic Acids Res. 32 : 1792 – 1797 . ↵ Garel, A. , Deleage, G. , Prudhomme, J.C. ( 1997 ) Structure and organization...
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Letter: Comparative genomic analyses of the human fungal pathogens Coccidioides and their relatives
- Thomas J. Sharpton,
- Jason E. Stajich,
- Steven D. Rounsley,
- Malcolm J. Gardner,
- Jennifer R. Wortman,
- Vinita S. Jordar,
- Rama Maiti,
- Chinnappa D. Kodira,
- Daniel E. Neafsey,
- Qiandong Zeng,
- Chiung-Yu Hung,
- Cody McMahan,
- Anna Muszewska,
- Marcin Grynberg,
- M. Alejandra Mandel,
- Ellen M. Kellner,
- Bridget M. Barker,
- John N. Galgiani,
- Marc J. Orbach,
- Theo N. Kirkland,
- Garry T. Cole,
- Matthew R. Henn,
- Bruce W. Birren,
- and John W. Taylor
Genome Res. October 2009 19: 1722-1731; Published in Advance August 28, 2009, doi:10.1101/gr.087551.108
..., respectively. Five distinct chromosomes, which accommodate 29 contigs, are seen in an optical map of the C. posadasii and support a higher estimate (Supplemental Fig. 1). TheC. immitis has seven supercontigs, but a whole- sequence alignment between C. immitis and C. posadasii supports an estimate of five...
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