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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
...history of C. Genome Research 1513 www..org Algorithms for multiple sequence alignment connecting to stub end nodes. Figure 2A shows an example adjacency graph containing two threads. Cactus graphs Let G0 be the adjacency graph for S, R, and;;. We briefly describe how G0 is transformed to a simplified...
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Methods: A novel method for multiple alignment of sequences with repeated and shuffled elements
- Benjamin Raphael,
- Degui Zhi,
- Haixu Tang,
- and Pavel Pevzner
Genome Res. November 2004 14: 2336-2346; doi:10.1101/gr.2657504
...representation produced by ABA is similar to the threaded blocksets recently introduced by Blanchette et al. ( 2004 ) to represent the complex multiple alignments of large genomic sequences. We demonstrate that ABA provides a solution to the open problem posed by Blanchette et al. ( 2004 ) of how...
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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
...al. 2004. Aligning multiple genomic sequences with the threaded blockset aligner. Genome Res. 14: 708–715. Bray, N. and Pachter, L. 2004. MAVID: Constrained ancestral alignment of multiple sequences. Genome Res. 14: 693–699. Bray, N., Dubchak, I., and Pachter, L. 2003. AVID: A global alignment...
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LETTER: Metrics of sequence constraint overlook regulatory sequences in an exhaustive analysis at phox2b
- David M. McGaughey,
- Ryan M. Vinton,
- Jimmy Huynh,
- Amr Al-Saif,
- Michael A. Beer,
- and Andrew S. McCallion
Genome Res. February 2008 18: 252-260; Published in Advance December 10, 2007, doi:10.1101/gr.6929408
...’s disease . Clin. Genet. 64 : 204 – 209 . ↵ Blanchette, M. , Kent, W.J. , Riemer, C. , Elnitski, L. , Smit, A.F. , Roskin, K.M. , Baertsch, R. , Rosenbloom, K. , Clawson, H. , Green, E.D. , et al. ( 2004 ) Aligning multiple genomic sequences with the threaded blockset aligner . Genome Res. 14 : 708 – 715...
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LETTER: Accelerated sequence divergence of conserved genomic elements in Drosophila melanogaster
- Alisha K. Holloway,
- David J. Begun,
- Adam Siepel,
- and Katherine S. Pollard
Genome Res. October 2008 18: 1592-1601; Published in Advance June 26, 2008, doi:10.1101/gr.077131.108
...Release 5 assembly as the reference sequence ( http://www.fruitfly.org/sequence/README.RELEASE5 ) were downloaded from the UCSC Genome Browser ( Karolchik et al. 2003 , 2004 ; Blanchette et al. 2004 ; http://.ucsc.edu/admin/cvs.html ). The multiple alignments were generated from high-quality pairwise...
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REVIEW: Multiple sequence alignment: In pursuit of homologous DNA positions
- Sudhir Kumar and
- Alan Filipski
Genome Res. February 2007 17: 127-135; doi:10.1101/gr.5232407
...sequences with the threaded blockset aligner . Genome Res. 14 : 708 – 715 . ↵ Boffelli, D. , McAuliffe, J. , Ovcharenko, D. , Lewis, K.D. , Ovcharenko, I. , Pachter, L. , Rubin, E.M. ( 2003 ) Phylogenetic shadowing of primate sequences to find functional regions of the human . Science 299 : 1391 – 1394...
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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
...Uncertainty in homology inferences: Assessing and improving genomic sequence alignment Gerton Lunter 1 , 3 , Andrea Rocco 2 , Naila Mimouni 2 , Andreas Heger 1 , Alexandre Caldeira 2 , and Jotun Hein 2 1 MRC...
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Methods: Græmlin: General and robust alignment of multiple large interaction networks
- Jason Flannick,
- Antal Novak,
- Balaji S. Srinivasan,
- Harley H. McAdams,
- and Serafim Batzoglou
Genome Res. September 2006 16: 1169-1181; Published in Advance August 9, 2006, doi:10.1101/gr.5235706
...-9051 10.1101/gr.5235706 genome;gr.5235706 Græmlin: General and robust alignment of multiple large interaction networks Græmlin: General and robust alignment of multiple large interaction networks Jason Flannick 1 , 4 , Antal Novak 1 , 4 , Balaji S. Srinivasan 2 , 3 , Harley H. McAdams 2 , and Serafim...
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Letter: Deeply conserved chordate noncoding sequences preserve genome synteny but do not drive gene duplicate retention
- Andrew L. Hufton,
- Susanne Mathia,
- Helene Braun,
- Udo Georgi,
- Hans Lehrach,
- Martin Vingron,
- Albert J. Poustka,
- and Georgia Panopoulou
Genome Res. November 2009 19: 2036-2051; Published in Advance August 24, 2009, doi:10.1101/gr.093237.109
...confirm that these PCNEs represent deeply conserved sequences, we calculated the phastCons score for each mouse PCNE using existing 17-way genomic alignments (Blanchette et al. 2004; Siepel et al. 2005; Kuhn et al. 2007). PhastCons assigns a score to each aligned base pair in multi alignments, ranging...
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Methods: Enredo and Pecan: Genome-wide mammalian consistency-based multiple alignment with paralogs
- Benedict Paten,
- Javier Herrero,
- Kathryn Beal,
- Stephen Fitzgerald,
- and Ewan Birney
Genome Res. November 2008 18: 1814-1828; Published in Advance October 10, 2008, doi:10.1101/gr.076554.108
...subsequences before applying standard pairwise alignment methods to join these segments. Finally TBA/MULTIZ ( Blanchette et al. 2004 ) uses a BLAST ( Altschul et al. 1990 ) like algorithm ( Schwartz et al. 2003 ) to find gapped local alignments, which it arranges together in a partially ordered block-set...
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