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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
...Cactus: Algorithms for genome multiple sequence alignment Benedict Paten 1 , Dent Earl , Ngan Nguyen , Mark Diekhans , Daniel Zerbino and David Haussler 1 Center for Biomolecular Science and Engineering, University...
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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
.... ↵ Bray, N. , Pachter, L. ( 2004 ) MAVID: Constrained ancestral alignment of multiple sequences . Genome Res. 14 : 693 – 699 . ↵ Brudno, M. , Do, C.B. , Cooper, G.M. , Kim, M.F. , Davydov, E. , Green, E.D. , Sidow, A. , Batzoglou, S. ( 2003a ) LAGAN and Multi-LAGAN: Efficient tools for large...
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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
...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 Batzoglou 1 , 5 1Department...
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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
...et al. 2003a ) uses a k -mer (each k -mer is an ungapped local alignment of length k ) chaining procedure to find initial local alignments around which a global alignment is constructed. Mavid ( Bray and Pachter 2004 ) recursively defines a global alignment using maximally nonrepetitive ungapped...
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Methods: Mauve: Multiple Alignment of Conserved Genomic Sequence With Rearrangements
- Aaron C.E. Darling,
- Bob Mau,
- Frederick R. Blattner,
- and Nicole T. Perna
Genome Res. July 2004 14: 1394-1403; doi:10.1101/gr.2289704
...). Similar multiple sequence alignment methods for long sequences have been developed and implemented in software packages such as MAVID, MLAGAN, and MGA ( Hohl et al. 2002 ; Bray and Pachter 2003 ; Brudno et al. 2003a ). All of these pairwise and multiple sequence aligners assume the input sequences...
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RESOURCE: Aligning Multiple Genomic Sequences With the Threaded Blockset Aligner
- Mathieu Blanchette,
- W. James Kent,
- Cathy Riemer,
- Laura Elnitski,
- Arian F.A. Smit,
- Krishna M. Roskin,
- Robert Baertsch,
- Kate Rosenbloom,
- Hiram Clawson,
- Eric D. Green,
- David Haussler,
- and Webb Miller
Genome Res. April 2004 14: 708-715; doi:10.1101/gr.1933104
..., J.M., Dehal, P., Christoffels, A., Rash, S., Hoon, S., Smit, A., et al. 2002 . Whole- shotgun assembly and analysis of the of Fugu rubripes. Science 297 : 1301 -1310. ↵ Bray, N. and Pachter, L. 2003 . MAVID multiple alignment server. Nucleic Acids Res. 31 : 3525 -3526. ↵ Brudno, M. and Morgenstern...
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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
.... The five score-based aligners we tested have each been designed with different purposes in mind, and the results reflect these design choices. For example, Mavid and Lagan are global aligners, and DiAlign was designed for aligning highly divergent sequence. The design aims of BLASTZ are the closest to our...
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PERSPECTIVE: Raising the estimate of functional human sequences
- Michael Pheasant and
- John S. Mattick
Genome Res. September 2007 17: 1245-1253; Published in Advance August 9, 2007, doi:10.1101/gr.6406307
...over different alignments (compare phastCons, BinCons, and GERP elements over TBA, MLAGAN, and MAVID alignments). A common objection to the possibility that mammalian s may contain large amounts of functional sequence under weak selection is the prediction that only strongly advantageous...
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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: Evolutionary constraints in conserved nongenic sequences of mammals
- Peter D. Keightley,
- Gregory V. Kryukov,
- Shamil Sunyaev,
- Daniel L. Halligan,
- and Daniel J. Gaffney
Genome Res. October 2005 15: 1373-1378; doi:10.1101/gr.3942005
...Spring Harbor Laboratory Press References ↵ Bejerano, G., Pheasant, M., Makunin, I., Stephen, S., Kent, W.J., Mattick, J.S. and Haussler, D. 2004 . Ultraconserved elements in the human . Science 304 : 1321 -1325. ↵ Bray, N. and Pachter, L. 2004 . MAVID: Constrained ancestral alignment of multiple...

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