The DOI matches its Crossref record; 6 of the 6 references it cites were found in a registry or an index.
Adaptive seeds tame genomic sequence comparison
Open accessAbstract
The main way of analyzing biological sequences is by comparing and aligning them to each other. It remains difficult, however, to compare modern multi-billionbase DNA data sets. The difficulty is caused by the nonuniform (oligo)nucleotide composition of these sequences, rather than their size per se. To solve this problem, we modified the standard seed-and-extend approach (e.g., BLAST) to use adaptive seeds. Adaptive seeds are matches that are chosen based on their rareness, instead of using fixed-length matches. This method guarantees that the number of matches, and thus the running time, increases linearly, instead of quadratically, with sequence length. LAST, our open source implementation of adaptive seeds, enables fast and sensitive comparison of large sequences with arbitrarily nonuniform composition.
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Cited by
MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability
Katoh, K., & Standley, D. M. (2013) · Molecular Biology and Evolution · doi:10.1093/molbev/mst010 · Cited by 46,209
Sensitive protein alignments at tree-of-life scale using DIAMOND
Buchfink, B., Reuter, K., & Drost, H.-G. (2021) · Nature Methods · doi:10.1038/s41592-021-01101-x · Cited by 5,097
MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets
Steinegger, M., & Söding, J. (2017) · Nature Biotechnology · doi:10.1038/nbt.3988 · Cited by 4,840
Reagent and laboratory contamination can critically impact sequence-based microbiome analyses
Salter, S. J., Cox, M. J., Turek, E. M., Calus, S. T., Cookson, W. O., Moffatt, M. F., Turner, P., Parkhill, J., Loman, N. J., & Walker, A. W. (2014) · BMC Biology · doi:10.1186/s12915-014-0087-z · Cited by 3,463
Nanopore sequencing technology, bioinformatics and applications
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Metadata
- Authors
- Kiełbasa, S. M., Wan, R., Sato, K., Horton, P., & Frith, M. C.
- Venue
- Genome Research
- Publisher
- Cold Spring Harbor Laboratory
- Published
- 2011-01-05
- Volume
- 21
- Issue
- 3
- Pages
- 487-493
- ISSN
- 1088-9051 (ISSN-L)
- OpenAlex
- W2162758337
- Cited by
- 1,281
- References
- 6
- Type
- posted content
- Language
- en
- Open access
- hybrid
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