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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
.... 2003 . Evolutionary conservation of regulatory elements in vertebrate Hox gene clusters. Genome Res. 13 : 1111 -1122. ↵ Schwartz, S., Zhang, Z., Frazer, K.A., Smit, A., Riemer, C., Bouck, J., Gibbs, R., Hardison, R.C., and Miller, W. 2000 . PipMaker—A web server for aligning two genomic DNA sequences...
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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
...by expressing Scl under the control of a stem cell enhancer. Development 128 : 4815 -4827. ↵ Schwartz, S., Zhang, Z., Frazer, K.A., Smit, A., Riemer, C., Bouck, J., Gibbs, R., Hardison, R., and Miller, W. 2000 . PipMaker—A web server for aligning two genomic DNA sequences. Genome Res. 10 : 577 -586. ↵ Schwartz...
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METHODS: LAGAN and Multi-LAGAN: Efficient Tools for Large-Scale Multiple Alignment of Genomic DNA
- Michael Brudno,
- Chuong B. Do,
- Gregory M. Cooper,
- Michael F. Kim,
- Eugene Davydov,
- NISC Comparative Sequencing Program,
- Eric D. Green,
- Arend Sidow,
- and Serafim Batzoglou
Genome Res. April 1, 2003 13: 721-731; Published in Advance March 12, 2003, doi:10.1101/gr.926603
...and chimpanzee), or very distant (e.g., human and fugu). Both programs are available for use on a public web server, http://lagan.stanford.edu , and are compatible with the VISTA visualization tool. The source code for LAGAN and MLAGAN is available from the authors. LAGAN and MLAGAN assume that one has already...
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RESOURCE: eShadow: A Tool for Comparing Closely Related Sequences
- Ivan Ovcharenko,
- Dario Boffelli,
- and Gabriela G. Loots
Genome Res. June 2004 14: 1191-1198; doi:10.1101/gr.1773104
...., and Miller, W. 2000 . PipMaker—A web server for aligning two genomic DNA sequences. Genome Res. 10 : 577 –586. ↵ Schwartz, S., Kent, W.J., Smit, A., Zhang, Z., Baertsch, R., Hardison, R.C., Haussler, D., and Miller, W. 2003 . Human—mouse alignments with BLASTZ. Genome Res. 13 : 103 –107. ↵ Shannon, M...
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ARTICLE: Identification and Characterization of Multi-Species Conserved Sequences
- Elliott H. Margulies,
- Mathieu Blanchette,
- NISC Comparative Sequencing Program,
- David Haussler,
- and Eric D. Green
Genome Res. December 2003 13: 2507-2518; doi:10.1101/gr.1602203
..., insertions were removed from the human reference sequence in each pair-wise alignment prior to building the MPA file. Note that we have also used the optimized alignment generated from the Web-based MultiPipMaker program and found that the MCSs detected with the two alignment strategies were ∼95% concordant...
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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
...for aligning long genomic DNA sequences. Several heuristic approaches to align long sequences have been developed under the assumption that highly similar subsequences can be found quickly and are likely to be part of the correct global alignment. These local alignments are used to anchor a global alignment...
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RESOURCE: GALA, a Database for Genomic Sequence Alignments and Annotations
- Belinda Giardine,
- Laura Elnitski,
- Cathy Riemer,
- Izabela Makalowska,
- Scott Schwartz,
- Webb Miller,
- and Ross C. Hardison
Genome Res. April 1, 2003 13: 732-741; doi:10.1101/gr.603103
...W. ( 2000 ) PipMaker—A Web server for aligning two genomic DNA sequences. Genome Res. 10 : 577 – 586 . ↵ Schwartz S. , Kent W.J. , Smit A. , Zhang Z. , Baertsch R. , Hardison R. , Haussler D. , Miller W. ( 2003 ) Human–mouse alignments with BLASTZ. Genome Res. 13 : 103 – 107 . ↵ Sherry S.T. , Ward M...
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Methods: Building Genomic Profiles for Uncovering Segmental Homology in the Twilight Zone
- Cedric Simillion,
- Klaas Vandepoele,
- Yvan Saeys,
- and Yves Van de Peer
Genome Res. June 2004 14: 1095-1106; doi:10.1101/gr.2179004
...based on different strategies. Generally, these methods can be divided into either alignment methods that align primary genomic DNA sequences or map-based methods that compare genetic or physical maps of genomic fragments. Alignment methods have the advantage that they can detect homology at the highest...
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LETTER: Evaluation of regulatory potential and conservation scores for detecting cis-regulatory modules in aligned mammalian genome sequences
- David C. King,
- James Taylor,
- Laura Elnitski,
- Francesca Chiaromonte,
- Webb Miller,
- and Ross C. Hardison
Genome Res. August 2005 15: 1051-1060; Published in Advance July 15, 2005, doi:10.1101/gr.3642605
...other sets of CRMs. The RP and phastCons scores are deposited in databases such as the Genome Browser ( Kent et al. 2002 ; Karolchik et al. 2004 ) and GALA ( Giardine et al. 2003 ; Elnitski et al. 2005 ), and MCS scores can be computed on a Web server. Investigators can apply the thresholds determined...
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LETTER: A functional survey of the enhancer activity of conserved non-coding sequences from vertebrate Iroquois cluster gene deserts
- Elisa de la Calle-Mustienes,
- Cármen Gloria Feijóo,
- Miguel Manzanares,
- Juan J. Tena,
- Elisa Rodríguez-Seguel,
- Annalisa Letizia,
- Miguel L. Allende,
- and José Luis Gómez-Skarmeta
Genome Res. August 2005 15: 1061-1072; Published in Advance July 15, 2005, doi:10.1101/gr.4004805
...cases. The high variability and relaxed sequence constraint of transcription factor DNA binding sites makes computational prediction of these cis -regulatory elements difficult, necessitating functional assays to describe them. A possible shortcut to this problem comes from the use of comparative...

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