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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
...relaxation determines how far away the method is able to explore from the constraining input alignment. To compare the predicted and true simulated ancestor sequences, we used Pecan ( Paten et al. 2008 ) to align them and then calculated three disagreement metrics from the resulting pairwise alignment...
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Resource: Cactus: Algorithms for genome multiple sequence alignment
- Benedict Paten,
- Dent Earl,
- Ngan Nguyen,
- Mark Diekhans,
- Daniel Zerbino,
- and David Haussler
Genome Res. September 2011 21: 1512-1528; Published in Advance June 10, 2011, doi:10.1101/gr.123356.111
...the Pecan global MSA program (Paten et al. 2009) (see Methods). The union of the set of end alignments for a group will potentially contain a degree of spuriousness, because each adjacency sequence is contained in two independent end alignments constructed without regard to each other. The second step...
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Resource: Alignathon: a competitive assessment of whole-genome alignment methods
- Dent Earl,
- Ngan Nguyen,
- Glenn Hickey,
- Robert S. Harris,
- Stephen Fitzgerald,
- Kathryn Beal,
- Igor Seledtsov,
- Vladimir Molodtsov,
- Brian J. Raney,
- Hiram Clawson,
- Jaebum Kim,
- Carsten Kemena,
- Jia-Ming Chang,
- Ionas Erb,
- Alexander Poliakov,
- Minmei Hou,
- Javier Herrero,
- William James Kent,
- Victor Solovyev,
- Aaron E. Darling,
- Jian Ma,
- Cedric Notredame,
- Michael Brudno,
- Inna Dubchak,
- David Haussler,
- and Benedict Paten
Genome Res. December 2014 24: 2077-2089; Published in Advance October 1, 2014, doi:10.1101/gr.174920.114
...simulation Mammal simulation Fly data set (real) AutoMZ AutoMZ Minmei Hau 1 1 1 Cactus Cactus Benedict Paten, Glenn Hickey 1 1 1 EPO Enredo, Pecan, Ortheus Stephen Fitzgerald, Kathryn Beal, Javier Herrero — 1 — Pecan Mercator, Pecan Stephen Fitzgerald, Kathryn Beal, Javier Herrero 1 1 — GenomeMatch Genome...
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Research: Impact of replication timing on non-CpG and CpG substitution rates in mammalian genomes
- Chun-Long Chen,
- Aurélien Rappailles,
- Lauranne Duquenne,
- Maxime Huvet,
- Guillaume Guilbaud,
- Laurent Farinelli,
- Benjamin Audit,
- Yves d'Aubenton-Carafa,
- Alain Arneodo,
- Olivier Hyrien,
- and Claude Thermes
Genome Res. April 2010 20: 447-457; Published in Advance January 26, 2010, doi:10.1101/gr.098947.109
...-specific alignments of Homo sapiens (assembly hg18), Pan troglodytes (panTro2), Pongo pygmaeus abelii (ponAbe2), and Macaca mulatta (rheMac2), that were generated using the Enredo Pecan Ortheus (EPO) pipeline (Paten et al. 2008a,b) were retrieved from the Ensembl Genome Browser (http://www.ensembl.org). Annotations...
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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
...technique with the alignments produced by the Penn State/UCSC Alignment Pipeline and displayed by the UCSC Genome Browser for two clades: vertebrates and Drosophila. We also compared our vertebrate alignments to the Enredo/Pecan alignments displayed at the Ensembl Genome Browser. To measure the alignment...
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Method: Structure-based whole-genome realignment reveals many novel noncoding RNAs
- Sebastian Will,
- Michael Yu,
- and Bonnie Berger
Genome Res. June 2013 23: 1018-1027; Published in Advance January 7, 2013, doi:10.1101/gr.137091.111
...of MERCATOR/PECAN WGAs more likely contain regions of low sequence identity, where purely sequence-based alignment would frequently misalign structural RNAs. For this reason, we conjecture that Mercator/Pecan will generally benefit from structure-based realignment more than MULTIZ. Furthermore, REAPR...
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Resource: Systematic detection of brain protein-coding genes under positive selection during primate evolution and their roles in cognition
- Guillaume Dumas,
- Simon Malesys,
- and Thomas Bourgeron
Genome Res. March 2021 31: 484-496; Published in Advance January 13, 2021, doi:10.1101/gr.262113.120
...with the reference We collected sequences and reconstructed sequence alignments with the reference human version hg19 (release 19, GRCh37.p13). For the primate common ancestor sequence, we used the Ensembl 6-way Enredo-Pecan-Ortheus (EPO) (Paten et al. 2008) multiple alignments v71, related to Homo sapiens (hg19...
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Research: Comprehensive identification and analysis of human accelerated regulatory DNA
- Rachel M. Gittelman,
- Enna Hun,
- Ferhat Ay,
- Jennifer Madeoy,
- Len Pennacchio,
- William S. Noble,
- R. David Hawkins,
- and Joshua M. Akey
Genome Res. September 2015 25: 1245-1255; Published in Advance June 23, 2015, doi:10.1101/gr.192591.115
...multiple functional genomics data sets to better understand the functional and biological characteristics of haDHSs. Results Framework for identifying conserved and human accelerated regulatory DNA To identify human accelerated regulatory DNA, we leveraged experimentally defined maps of DHSs from 130 cell...
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RESOURCE: An effective model for natural selection in promoters
- Michael M. Hoffman and
- Ewan Birney
Genome Res. May 2010 20: 685-692; Published in Advance March 1, 2010, doi:10.1101/gr.096719.109
...neutrality in the age of genomics. Heredity 86: 641–647. Paten B, Herrero J, Beal K, Fitzgerald S, Birney E. 2008. Enredo and Pecan: Genome-wide mammalian consistency-based multiple alignment with paralogs. Genome Res 18: 1814–1828. Pennacchio LA, AhituvN,Moses AM, Prabhakar S, NobregaMA, Shoukry...
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Resource: Detecting copy number variation with mated short reads
- Paul Medvedev,
- Marc Fiume,
- Misko Dzamba,
- Tim Smith,
- and Michael Brudno
Genome Res. November 2010 20: 1613-1622; Published in Advance August 30, 2010, doi:10.1101/gr.106344.110
...variables as follows: The jth region of the ith block is stored as the closed interval partition(i,j). Furthermore, for each block, we label the endpoints of each of its regions with s and t in such a way that the s ends of all the regions represent the same endpoint of the multiple alignment. We thus have...

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