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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
..., this approach ensures the detection of evolutionarily conserved elements throughout the alignment even if orthologous regions have been repositioned or inverted in only a subset of the input species. Mulan alignment visualization is based on the zPicture display design ( Ovcharenko et al. 2004b ), where...
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Method: Genome-wide identification of conserved regulatory function in diverged sequences
- Leila Taher,
- David M. McGaughey,
- Samantha Maragh,
- Ivy Aneas,
- Seneca L. Bessling,
- Webb Miller,
- Marcelo A. Nobrega,
- Andrew S. McCallion,
- and Ivan Ovcharenko
Genome Res. July 2011 21: 1139-1149; Published in Advance May 31, 2011, doi:10.1101/gr.119016.110
...by searching for conserved TFBS arrangements. With an estimated 5% false-positive rate (FPR) in approximately 3000 human and zebrafish syntenic loci, we detected approximately 300 pairs of diverged elements that are likely to share common ancestry and have similar regulatory activity. By analyzing a pool...
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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
...-range enhancers. Science 302 : 413 . ↵ Ovcharenko, I., Loots, G.G., Hardison, R.C., Miller, W., and Stubbs, L. 2004 . zPicture: Dynamic alignment and visualization tool for analyzing conservation profiles. Genome Res. 14 : 472 –477. ↵ Pennacchio, L.A., Olivier, M., Hubacek, J.A., Cohen, J.C., Cox, D.R., Fruchart...
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RESOURCE: Galaxy: A platform for interactive large-scale genome analysis
- Belinda Giardine,
- Cathy Riemer,
- Ross C. Hardison,
- Richard Burhans,
- Laura Elnitski,
- Prachi Shah,
- Yi Zhang,
- Daniel Blankenberg,
- Istvan Albert,
- James Taylor,
- Webb Miller,
- W. James Kent,
- and Anton Nekrutenko
Genome Res. October 2005 15: 1451-1455; Published in Advance September 16, 2005, doi:10.1101/gr.4086505
...and characterization of multi-species conserved sequences. Genome Res. 13 : 2507 -2518. ↵ Ovcharenko, I., Loots, G.G., Hardison, R.C., Miller, W., and Stubbs, L. 2004 . zPicture: Dynamic alignment and visualization tool for analyzing conservation profiles. Genome Res. 14 : 472 -477. ↵ Presgraves, D.C., Balagopalan, L...
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ARTICLE: Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes
- Adam Siepel,
- Gill Bejerano,
- Jakob S. Pedersen,
- Angie S. Hinrichs,
- Minmei Hou,
- Kate Rosenbloom,
- Hiram Clawson,
- John Spieth,
- LaDeana W. Hillier,
- Stephen Richards,
- George M. Weinstock,
- Richard K. Wilson,
- Richard A. Gibbs,
- W. James Kent,
- Webb Miller,
- and David Haussler
Genome Res. August 2005 15: 1034-1050; Published in Advance July 15, 2005, doi:10.1101/gr.3715005
...such as VISTA ( Mayor et al. 2000 ), PipMaker ( Schwartz et al. 2000 ), and zPicture ( Ovcharenko et al. 2004 ) can be used to construct alignments, visualize annotations and percent identity levels, and/or define conserved elements according to length and identity thresholds. As more s have become available...
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LETTER: Genomic deletion of a long-range bone enhancer misregulates sclerostin in Van Buchem disease
- Gabriela G. Loots,
- Michaela Kneissel,
- Hansjoerg Keller,
- Myma Baptist,
- Jessie Chang,
- Nicole M. Collette,
- Dmitriy Ovcharenko,
- Ingrid Plajzer-Frick,
- and Edward M. Rubin
Genome Res. July 2005 15: 928-935; Published in Advance June 17, 2005, doi:10.1101/gr.3437105
...gene. Genome Res. 13 : 2069 -2081. ↵ Nobrega, M.A., Ovcharenko, I., Afzal, V., and Rubin, E.M. 2003 . Scanning human gene deserts for long-range enhancers. Science 302 : 413 . ↵ Ovcharenko, I., Loots, G.G., Hardison, R.C., Miller, W., and Stubbs, L. 2004 . zPicture: Dynamic alignment and visualization...
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LETTER: Defining the mammalian CArGome
- Qiang Sun,
- Guang Chen,
- Jeffrey W. Streb,
- Xiaochun Long,
- Yumei Yang,
- Christian J. Stoeckert, Jr.,
- and Joseph M. Miano
Genome Res. February 2006 16: 197-207; Published in Advance December 19, 2005, doi:10.1101/gr.4108706
...) and 10,309 mouse (mm3) RefSeq transcripts. We used LAGAN to align the retrieved genomic sequences of each human-mouse ortholog pair and arbitrarily set the conservation threshold at 80% with a 50-bp scan window. Based on published data accumulated over the last 20 years on the composition of functional...

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