The DOI matches its Crossref record; 6 of the 6 references it cites were found in a registry or an index.
Using DECIPHER v2.0 to Analyze Big Biological Sequence Data in R
Open accessAbstract
In recent years, the cost of DNA sequencing has decreased at a rate that has outpaced improvements in memory capacity.It is now common to collect or have access to many gigabytes of biological sequences.This has created an urgent need for approaches that analyze sequences in subsets without requiring all of the sequences to be loaded into memory at one time.It has also opened opportunities to improve the organization and accessibility of information acquired in sequencing projects.The DECIPHER package offers solutions to these problems by assisting in the curation of large sets of biological sequences stored in compressed format inside a database.This approach has many practical advantages over standard bioinformatics workflows, and enables large analyses that would otherwise be prohibitively time consuming.
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Cites
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
Altschul, S. (1997) · Nucleic Acids Research · doi:10.1093/nar/25.17.3389 · Cited by 73,302
Reducing the Effects of PCR Amplification and Sequencing Artifacts on 16S rRNA-Based Studies
Schloss, P. D., Gevers, D., & Westcott, S. L. (2011) · PLoS ONE · doi:10.1371/journal.pone.0027310 · Cited by 2,112
DECIPHER: harnessing local sequence context to improve protein multiple sequence alignment
Wright, E. S. (2015) · BMC Bioinformatics · doi:10.1186/s12859-015-0749-z · Cited by 385
Self-citationCompression of next-generation sequencing reads aided by highly efficient de novo assembly
Jones, D. C., Ruzzo, W. L., Peng, X., & Katze, M. G. (2012) · Nucleic Acids Research · doi:10.1093/nar/gks754 · Cited by 161
Data compression for sequencing data
Deorowicz, S., & Grabowski, S. (2013) · Algorithms for Molecular Biology · doi:10.1186/1748-7188-8-25 · Cited by 85
Wandelt, S., Bux, M., & Leser, U. (2014) · Current Bioinformatics · doi:10.2174/1574893609666140516010143 · Cited by 56
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Anand, R. P., Layer, J. V., Heja, D., Hirose, T., Lassiter, G., Firl, D. J., Paragas, V. B., Akkad, A., Chhangawala, S., Colvin, R. B., et al. (2023) · Nature · doi:10.1038/s41586-023-06594-4 · Cited by 302
Microbial composition and functional diversity differ across urban green infrastructure types
Gill, A. S., Purnell, K., Palmer, M. I., Stein, J., & McGuire, K. L. (2020) · Frontiers in Microbiology · doi:10.3389/fmicb.2020.00912 · Cited by 64
Lecoeuvre, A., Ménez, B., Cannat, M., Chavagnac, V., & Gérard, E. (2021) · The ISME Journal · doi:10.1038/s41396-020-00816-7 · Cited by 62
Keskitalo, A., Aatsinki, A.-K., Kortesluoma, S., Pelto, J., Korhonen, L., Lahti, L., Lukkarinen, M., Munukka, E., Karlsson, H., & Karlsson, L. (2021) · Stress · doi:10.1080/10253890.2021.1895110 · Cited by 44
Castro-Severyn, J., Pardo-Esté, C., Mendez, K. N., Fortt, J., Marquez, S., Molina, F., Castro-Nallar, E., Remonsellez, F., & Saavedra, C. P. (2021) · Microbiology Spectrum · doi:10.1128/spectrum.00444-21 · Cited by 36
Metadata
- Authors
- Wright, E.
- Venue
- The R Journal
- Publisher
- The R Foundation
- Published
- 2016
- Volume
- 8
- Issue
- 1
- Pages
- 352
- ISSN
- 2073-4859 (ISSN-L)
- OpenAlex
- W2785846143
- Cited by
- 1,016
- References
- 6
- FWCI
- 9.63
- Type
- journal article
- Language
- en
- Open access
- hybrid
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Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
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