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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
...Multiple whole-genome alignments without a reference organism Inna Dubchak 1 , 2 , Alexander Poliakov 1 , Andrey Kislyuk 3 and Michael Brudno 4 , 5 1 Genome Sciences Division, Lawrence Berkeley National Laboratory, Berkeley...
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LETTER: Strategies and Tools for Whole-Genome Alignments
- Olivier Couronne,
- Alexander Poliakov,
- Nicolas Bray,
- Tigran Ishkhanov,
- Dmitriy Ryaboy,
- Edward Rubin,
- Lior Pachter,
- and Inna Dubchak
Genome Res. January 1, 2003 13: 73-80; doi:10.1101/gr.762503
...al. 2002 ) was aligned to the human using the BLAST program ( Aetshul et al. 1990 ), but the complexity of the problem was mitigated by the small size of the Fugu and its relatively simple repeat structure. A similar local alignment approach was applied to the mouse by the BLASTZ group ( Schwartz et...
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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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Resource: Comparing genomic and epigenomic features across species using the WashU Comparative Epigenome Browser
- Xiaoyu Zhuo,
- Silas Hsu,
- Deepak Purushotham,
- Prashant Kumar Kuntala,
- Jessica K. Harrison,
- Alan Y. Du,
- Samuel Chen,
- Daofeng Li,
- and Ting Wang
Genome Res. May 2023 33: 824-835; Published in Advance May 8, 2023, doi:10.1101/gr.277550.122
.... It is straightforward to visualize single-nucleotide variations (SNVs) and short insertions/deletions (indels) between the two assemblies (Fig. 2A).View larger version: In this window In a new window Figure 2. Displaying alignments using the WashU Comparative Epi Browser. (A) Displaying hg38-mm10 BLASTZ alignment...
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ARTICLE: Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome
- Elliott H. Margulies,
- Gregory M. Cooper,
- George Asimenos,
- Daryl J. Thomas,
- Colin N. Dewey,
- Adam Siepel,
- Ewan Birney,
- Damian Keefe,
- Ariel S. Schwartz,
- Minmei Hou,
- James Taylor,
- Sergey Nikolaev,
- Juan I. Montoya-Burgos,
- Ari Löytynoja,
- Simon Whelan,
- Fabio Pardi,
- Tim Massingham,
- James B. Brown,
- Peter Bickel,
- Ian Holmes,
- James C. Mullikin,
- Abel Ureta-Vidal,
- Benedict Paten,
- Eric A. Stone,
- Kate R. Rosenbloom,
- W. James Kent,
- Gerard G. Bouffard,
- Xiaobin Guan,
- Nancy F. Hansen,
- Jacquelyn R. Idol,
- Valerie V.B. Maduro,
- Baishali Maskeri,
- Jennifer C. McDowell,
- Morgan Park,
- Pamela J. Thomas,
- Alice C. Young,
- Robert W. Blakesley,
- Donna M. Muzny,
- Erica Sodergren,
- David A. Wheeler,
- Kim C. Worley,
- Huaiyang Jiang,
- George M. Weinstock,
- Richard A. Gibbs,
- Tina Graves,
- Robert Fulton,
- Elaine R. Mardis,
- Richard K. Wilson,
- Michele Clamp,
- James Cuff,
- Sante Gnerre,
- David B. Jaffe,
- Jean L. Chang,
- Kerstin Lindblad-Toh,
- Eric S. Lander,
- Angie Hinrichs,
- Heather Trumbower,
- Hiram Clawson,
- Ann Zweig,
- Robert M. Kuhn,
- Galt Barber,
- Rachel Harte,
- Donna Karolchik,
- Matthew A. Field,
- Richard A. Moore,
- Carrie A. Matthewson,
- Jacqueline E. Schein,
- Marco A. Marra,
- Stylianos E. Antonarakis,
- Serafim Batzoglou,
- Nick Goldman,
- Ross Hardison,
- David Haussler,
- Webb Miller,
- Lior Pachter,
- Eric D. Green,
- and Arend Sidow
Genome Res. June 2007 17: 760-774; doi:10.1101/gr.6034307
...Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome Elliott H. Margulies 2 , 8 , 21 , 7 , Gregory M. Cooper 2 , 3 , 9 , George Asimenos 2 , 10 , Daryl J. Thomas 2 , 11 , 12 , Colin N...
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METHODS: SGP-1: Prediction and Validation of Homologous Genes Based on Sequence Alignments
- Thomas Wiehe,
- Steffi Gebauer-Jung,
- Thomas Mitchell-Olds,
- and Roderic Guigó
Genome Res. September 1, 2001 11: 1574-1583; doi:10.1101/gr.177401
.... This modularity makes the tool very fast and versatile: given a suitable format-conversion tool, SGP-1 may be combined with any pairwise alignment program. We successfully ran SGP-1 on alignments produced by SIM96 ( Huang and Miller 1991 ), BLASTN , TBLASTX ( Altschul et al. 1990 ), BLASTZ (W. Miller, pers. comm...
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LETTER: Identification of Candidate Disease Genes by EST Alignments, Synteny, and Expression and Verification of Ensembl Genes on Rat Chromosome 1q43-54
- Ursula Vitt,
- Darryl Gietzen,
- Kristian Stevens,
- Jim Wingrove,
- Shanya Becha,
- Sean Bulloch,
- John Burrill,
- Narinder Chawla,
- Jennifer Chien,
- Matthew Crawford,
- Craig Ison,
- Liam Kearney,
- Mary Kwong,
- Joe Park,
- Jennifer Policky,
- Mark Weiler,
- Renee White,
- Yuming Xu,
- Sue Daniels,
- Howard Jacob,
- Michael I. Jensen-Seaman,
- Jozef Lazar,
- Laura Stuve,
- and Jeanette Schmidt
Genome Res. April 2004 14: 640-650; doi:10.1101/gr.1932304
...Identification of Candidate Disease Genes by EST Alignments, Synteny, and Expression and Verification of Ensembl Genes on Rat Chromosome 1q43-54 Ursula Vitt 1 , 3 , Darryl Gietzen 1 , Kristian Stevens 1 , Jim Wingrove 1 , Shanya Becha 1...
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Resource: Interspecies regulatory landscapes and elements revealed by novel joint systematic integration of human and mouse blood cell epigenomes
- Guanjue Xiang,
- Xi He,
- Belinda M. Giardine,
- Kathryn J. Isaac,
- Dylan J. Taylor,
- Rajiv C. McCoy,
- Camden Jansen,
- Cheryl A. Keller,
- Alexander Q. Wixom,
- April Cockburn,
- Amber Miller,
- Qian Qi,
- Yanghua He,
- Yichao Li,
- Jens Lichtenberg,
- Elisabeth F. Heuston,
- Stacie M. Anderson,
- Jing Luan,
- Marit W. Vermunt,
- Feng Yue,
- Michael E.G. Sauria,
- Michael C. Schatz,
- James Taylor,
- Berthold Göttgens,
- Jim R. Hughes,
- Douglas R. Higgs,
- Mitchell J. Weiss,
- Yong Cheng,
- Gerd A. Blobel,
- David M. Bodine,
- Yu Zhang,
- Qunhua Li,
- Shaun Mahony,
- and Ross C. Hardison
Genome Res. July 2024 34: 1089-1105; Published in Advance July 1, 2024, doi:10.1101/gr.277950.123
...and correlations of epigenetic states in human GATA1 and mouse Gata1 genes and flanking genes. (A) Dot-plot view of chained BLASTZ alignments by PipMaker (Schwartz et al. 2000) between genomic intervals encompassing and surrounding the human GATA1 (GRCh38 Chr X: 48,760,001–48,836,000; 76 kb) and mouse Gata1 (mm10...
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ERRATUM: Correction for Volume 13, p. 103 Genome Res. April 2004 14: 786

...genome;14/4/786 1088-9051 Correction for Volume 13, p. 103 Correction for Volume 13, p. 103 Genome Research 13: 103-107 (2003) Human-Mouse Alignments With BLASTZ Scott Schwartz, W. James Kent, Arian Smit, Zheng Zhang, Robert Baertsch, Ross C. Hardison, David Haussler, and Webb Miller In the second...
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Research: Conserved non-AUG uORFs revealed by a novel regression analysis of ribosome profiling data
- Pieter Spealman,
- Armaghan W. Naik,
- Gemma E. May,
- Scott Kuersten,
- Lindsay Freeberg,
- Robert F. Murphy,
- and Joel McManus
Genome Res. February 2018 28: 214-222; Published in Advance December 18, 2017, doi:10.1101/gr.221507.117
.... Nature 512: 208–212. ↵Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC, Haussler D, Miller W. 2003. Human–mouse alignments with BLASTZ. Genome Res 13: 103–107. ↵Selpi, Bryant CH, Kemp GJL, Sarv J, Kristiansson E, Sunnerhagen P. 2009. Predicting functional upstream open reading frames...
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