Strategies and tools for whole-genome alignments
Open accessAbstract
The availability of the assembled mouse genome makes possible, for the first time, an alignment and comparison of two large vertebrate genomes. We investigated different strategies of alignment for the subsequent analysis of conservation of genomes that are effective for assemblies of different quality. These strategies were applied to the comparison of the working draft of the human genome with the Mouse Genome Sequencing Consortium assembly, as well as other intermediate mouse assemblies. Our methods are fast and the resulting alignments exhibit a high degree of sensitivity, covering more than 90% of known coding exons in the human genome. We obtained such coverage while preserving specificity. With a view towards the end user, we developed a suite of tools and Web sites for automatically aligning and subsequently browsing and working with whole-genome comparisons. We describe the use of these tools to identify conserved non-coding regions between the human and mouse genomes, some of which have not been identified by other methods.
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With the rapid advancements in sequencing technologies and the ever-increasing amount of genomic data, the development of efficient and accurate WGA algorithms has become more critical than ever.
“With the rapid advancements in sequencing technologies and the ever-increasing amount of genomic data, the development of efficient and accurate WGA algorithms has become more critical than ever [67].”
From Whole-Genome Alignment: Methods, Challenges, and Future Directions (2024) · cites this paper as [67]
The Abstract (page not available) says large genomes make many existing alignment algorithms inefficient and complicate accurate identification of orthologous regions; it presents a rapid, specific whole-genome alignment method. The paper does not establish that advances in sequencing technology or an ever-increasing volume of genomic data have made algorithm development more critical than ever. (LLM, conf=0.82)
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Initial sequencing and comparative analysis of the mouse genome
Mouse Genome Sequencing Consortium (2002) · Nature · doi:10.1038/nature01262 · Cited by 7,187 · see citing works
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Research works printed but not linked: 2
- Lawn, R.M., Schwartz, K., and Patthy, L. 1997. Convergent evolution of apolipoprotein(a) in primates and hedgehog. Proc. Natl. Acad. Sci. 94: 11992-11997.
- WEB SITE REFERENCES http://pipeline.lbl.gov; comparative analysis pipeline gateway at Lawrence Berkeley National laboratory. http://pipeline.lbl.gov/cgi-bin/cnc; database of conserved sequences from LBNL, PSU, and UCSC. http://bio.math.berkeley.edu/avid; Avid Web site. http://genome.ucsc.edu/; UCSC Web site from which the human genome assemblies used in this study where downloaded. http://www.ncbi.nlm.nih.gov/LocusLink/; NCBI Locus Link. http://pipeline.lbl.gov/downloads.shtml; Download page for whole- genome alignments and other materials. http://www.ensembl.org; The ENSEMBL project Web site. http://pipeline.lbl.gov/das.shtnl; Alignment DAS server. http://bio.cse.psu.edu; BLASTZ.
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Whole-Genome Alignment: Methods, Challenges, and Future Directions
Saada, B., Zhang, T., Siga, E., Zhang, J., & Magalhães Muniz, M. M. (2024) · Applied Sciences · doi:10.3390/app14114837 · Cited by 15 · see citing works
- Authors
- Couronne, O., Poliakov, A., Bray, N., Ishkhanov, T., Ryaboy, D., Rubin, E., Pachter, L., & Dubchak, I.
- Affiliations
- Lawrence Berkeley National Laboratory (US)
- Venue
- Genome Research
- Publisher
- Cold Spring Harbor Laboratory
- Published
- 2003-01-01
- Volume
- 13
- Issue
- 1
- Pages
- 73-80
- ISSN
- 1088-9051 (ISSN-L)
- 1549-5469
- PMC
- PMC430965
- OpenAlex
- W4301509649
- Cited by
- 224
- References
- 1
- Citations by year
- 2026: 1 · 2024: 3 · 2023: 4 · 2022: 1 · 2021: 3 · 2020: 2 · 2019: 7 · 2018: 2 · 2017: 1 · 2016: 2 · 2015: 2 · 2014: 3 · 2013: 4 · 2012: 5
- Type
- posted content
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- Genome Research (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- OSTI OAI (U.S. Department of Energy Office of Scientific and Technical Information) (submittedVersion)
- University of North Texas Digital Library (University of North Texas) (submittedVersion)
- CaltechAUTHORS (California Institute of Technology) (submittedVersion, cc-by-nc)
- eScholarship (California Digital Library) (submittedVersion)
- Funders
- U.S. Department of Energy (DE-AC03-?, AC03-76SF00098, DEAC03-76SF00098)
- University of Pennsylvania
- Pennsylvania State University
- Office of Science (DEAC03-76SF00098)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genome Rearrangement Algorithms
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Fractal and DNA sequence analysis
- Keywords
- whole-genome alignment, genome conservation, alignment tools, comparative genomics, genome assembly quality
- MeSH terms
- Algorithms, Animals, Chromosomes, Chromosomes, Human, Computer Communication Networks, Humans, Research Design, Software, Genome, Human, Sequence Alignment, Genome, Internet, Databases, Genetic, Mice
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