The DOI matches its Crossref record; 4 of the 4 references it cites were found in a registry or an index.
AVID: A Global Alignment Program
Open accessAbstract
In this paper we describe a new global alignment method called AVID. The method is designed to be fast, memory efficient, and practical for sequence alignments of large genomic regions up to megabases long. We present numerous applications of the method, ranging from the comparison of assemblies to alignment of large syntenic genomic regions and whole genome human/mouse alignments. We have also performed a quantitative comparison of AVID with other popular alignment tools. To this end, we have established a format for the representation of alignments and methods for their comparison. These formats and methods should be useful for future studies. The tools we have developed for the alignment comparisons, as well as the AVID program, are publicly available. See Web Site References section for AVID Web address and Web addresses for other programs discussed in this paper.
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Cites
Needleman, S. B., & Wunsch, C. D. (1970) · Journal of Molecular Biology · doi:10.1016/0022-2836(70)90057-4 · Cited by 11,288
Initial sequencing and comparative analysis of the mouse genome
Mouse Genome Sequencing Consortium (2002) · Nature · doi:10.1038/nature01262 · Cited by 7,187
Fast algorithms for large-scale genome alignment and comparison
Delcher, A. L. (2002) · Nucleic Acids Research · doi:10.1093/nar/30.11.2478 · Cited by 1,036
Strategies and tools for whole-genome alignments
Couronne, O., Poliakov, A., Bray, N., Ishkhanov, T., Ryaboy, D., Rubin, E., Pachter, L., & Dubchak, I. (2003) · Genome Research · doi:10.1101/gr.762503 · Cited by 224
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Versatile and open software for comparing large genomes
Kurtz, S., Phillippy, A., Delcher, A. L., Smoot, M., Shumway, M., Antonescu, C., & Salzberg, S. L. (2004) · Genome Biology · doi:10.1186/gb-2004-5-2-r12 · Cited by 5,254
John, B., Enright, A. J., Aravin, A., Tuschl, T., Sander, C., & Marks, D. S. (2004) · PLoS Biology · doi:10.1371/journal.pbio.0020363 · Cited by 3,796
MicroRNA targets in Drosophila
Enright, A. J., John, B., Gaul, U., Tuschl, T., Sander, C., & Marks, D. S. (2003) · Genome Biology · doi:10.1186/gb-2003-5-1-r1 · Cited by 3,597
GMAP: A genomic mapping and alignment program for mRNA and EST sequences
Wu, T. D., & Watanabe, C. K. (2005) · Bioinformatics · doi:10.1093/bioinformatics/bti310 · Cited by 2,354
Transcriptional regulation by calcium, calcineurin, and NFAT
Hogan, P. G., Chen, L., Nardone, J., & Rao, A. (2003) · Genes & Development · doi:10.1101/gad.1102703 · Cited by 1,991
Metadata
- Authors
- Bray, N., Dubchak, I., & Pachter, L.
- Venue
- Genome Research
- Publisher
- Cold Spring Harbor Laboratory
- Published
- 2002-12-30
- Volume
- 13
- Issue
- 1
- Pages
- 97-102
- ISSN
- 1088-9051 (ISSN-L)
- 1549-5469
- OpenAlex
- W2110291136
- Cited by
- 495
- References
- 4
- Type
- posted content
- Language
- en
- Open access
- bronze
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