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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
.../A, termed its ‘‘reverse complement,’’ and similarly G/C from its reverse complement C/G, using signs we hence can equivalentlywrite#2;A/T=T/A,#2;T/A =A/T,#2;G/C =C/G, and#2;C/G = G/C. A DNA sequence is a member of the set p#3;= n=0 p n of finite sequences over the alphabet p. We write xi to represent...
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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
...conserved blocks. Programs compared for homology accuracy are ClustalW ( Thompson et al. 1994 ), BLASTZ ( Schwartz et al. 2003 ), DiAlign ( Morgenstern 1999 ), and Lagan ( Brudno et al. 2003a ). Limits on the homology accuracy in Figure 3A are for DNA segments in which all positions are evolving strictly...
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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
...sequence with rearrangements permitted in the other sequence. Although Shuffle-LAGAN's alignment approach works for pairwise comparison, an extension of the method to multiple sequences has not yet been suggested. MultiPipMaker, based on BLASTZ, is a tool that can align multiple s to a single reference...
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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
...study of pairwise alignments of genomic DNA at human–mouse divergence. We find that &gt;15% of aligned bases are incorrect in existing whole-genome alignments, and we identify three types of alignment error, each leading to systematic biases in all algorithms considered. Careful modeling...
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Methods: MAVID: Constrained Ancestral Alignment of Multiple Sequences
- Nicolas Bray and
- Lior Pachter
Genome Res. April 2004 14: 693-699; doi:10.1101/gr.1960404
...and Multi-LAGAN: Efficient tools for large-scale multiple alignment of genomic DNA. Genome Res. 13 : 721 -731. ↵ Burge, C. and Karlin, S. 1997 . Prediction of complete gene structures in human genomic DNA. J. Mol. Biol. 268 : 78 -94. ↵ Chakrabarti, K. and Pachter, L. 2004 . Visualization of multiple...
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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
...that the unknown protein shares function with the landmark protein. Figure 6 shows an example of functional annotation through both pairwise and multiple network alignment. The pairwise alignment between E. coli and C. crescentus ( Fig. 6A ) shows a conserved DNA replication module. This includes the components...
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Methods: Automated Whole-Genome Multiple Alignment of Rat, Mouse, and Human
- Michael Brudno,
- Alexander Poliakov,
- Asaf Salamov,
- Gregory M. Cooper,
- Arend Sidow,
- Edward M. Rubin,
- Victor Solovyev,
- Serafim Batzoglou,
- and Inna Dubchak
Genome Res. April 2004 14: 685-692; doi:10.1101/gr.2067704
...Comparative Sequencing Program. 2003a . LAGAN and Multi-LAGAN: Efficient tools for large-scale multiple alignment of genomic DNA. Genome Res. 13 : 721 -731. ↵ Brudno, M., Malde, S., Poliakov, A., Do, C.B., Couronne, O., Dubchak, I., and Batzoglou, S. 2003b . Glocal alignment: Finding rearrangements during...
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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
...of the methods. Pecan implements the same basic objective function as the amino acid aligner Probcons ( Do et al. 2005 ) does. We briefly review this function. Let π represent the basic symbol alphabet (i.e. { A , C , T , G } for DNA). A sequence represents a member of ∪ π i , where π i represents the set of all...
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RESOURCE: Analysis of Multiple Genomic Sequence Alignments: A Web Resource, Online Tools, and Lessons Learned From Analysis of Mammalian SCL Loci
- Michael A. Chapman,
- Ian J. Donaldson,
- James Gilbert,
- Darren Grafham,
- Jane Rogers,
- Anthony R. Green,
- and Berthold Göttgens
Genome Res. February 2004 14: 313-318; Published in Advance January 12, 2004, doi:10.1101/gr.1759004
...., and Rubin, E.M. 2003 . Phylogenetic shadowing of primate sequences to find functional regions of the human . Science 299 : 1391 -1394. ↵ Brudno, M., Do, C.B., Cooper, G.M., Kim, M.F., Davydov, E., Green, E.D., Sidow, A., and Batzoglou, S. 2003 . LAGAN and Multi-LAGAN: Efficient tools for large-scale...
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Chicken Special/Resources: Mulan: Multiple-sequence local alignment and visualization for studying function and evolution
- Ivan Ovcharenko,
- Gabriela G. Loots,
- Belinda M. Giardine,
- Minmei Hou,
- Jian Ma,
- Ross C. Hardison,
- Lisa Stubbs,
- and Webb Miller
Genome Res. January 2005 15: 184-194; Published in Advance December 8, 2004, doi:10.1101/gr.3007205
...assembly as the reference sequence. In sharp contrast to several other available global multiple-sequence alignment tools, the threaded blockset alignment strategy implemented by Mulan detects and properly processes DNA rearrangements often characteristic of synteny among distantly related s. Also...

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