The DOI matches its Crossref record; 1 of the 1 references it cites were found in a registry or an index.
A Fast and Symmetric DUST Implementation to Mask Low-Complexity DNA Sequences
Abstract
The DUST module has been used within BLAST for many years to mask low-complexity sequences. In this paper, we present a new implementation of the DUST module that uses the same function to assign a complexity score to a sequence, but uses a different rule by which high-scoring sequences are masked. The new rule masks every nucleotide masked by the old rule and occasionally masks more. The new masking rule corrects two related deficiencies with the old rule. First, the new rule is symmetric with respect to reversing the sequence. Second, the new rule is not context sensitive; the decision to mask a subsequence does not depend on what sequences flank it. The new implementation is at least four times faster than the old on the human genome. We show that both the percentage of additional bases masked and the effect on MegaBLAST outputs are very small.
Overview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
Cites
Tandem repeats finder: a program to analyze DNA sequences
Benson, G. (1999) · Nucleic Acids Research · doi:10.1093/nar/27.2.573 · Cited by 9,374
Cited by
BLAST+: architecture and applications
Camacho, C., Coulouris, G., Avagyan, V., Ma, N., Papadopoulos, J., Bealer, K., & Madden, T. L. (2009) · BMC Bioinformatics · doi:10.1186/1471-2105-10-421 · Cited by 22,074
The Ensembl gene annotation system
Aken, B. L., Ayling, S., Barrell, D., Clarke, L., Curwen, V., Fairley, S., Fernandez Banet, J., Billis, K., García Girón, C., Hourlier, T., et al. (2016) · Database · doi:10.1093/database/baw093 · Cited by 1,086
Intermittent Fasting Confers Protection in CNS Autoimmunity by Altering the Gut Microbiota
Cignarella, F., Cantoni, C., Ghezzi, L., Salter, A., Dorsett, Y., Chen, L., Phillips, D., Weinstock, G. M., Fontana, L., Cross, A. H., et al. (2018) · Cell Metabolism · doi:10.1016/j.cmet.2018.05.006 · Cited by 568
The sheep genome illuminates biology of the rumen and lipid metabolism
Jiang, Y., Xie, M., Chen, W., Talbot, R., Maddox, J. F., Faraut, T., Wu, C., Muzny, D. M., Li, Y., Zhang, W., et al. (2014) · Science · doi:10.1126/science.1252806 · Cited by 514
The design and construction of reference pangenome graphs with minigraph
Li, H., Feng, X., & Chu, C. (2020) · Genome Biology · doi:10.1186/s13059-020-02168-z · Cited by 455
Metadata
- Authors
- Morgulis, A., Gertz, E. M., Schäffer, A. A., & Agarwala, R.
- Venue
- Journal of Computational Biology
- Publisher
- SAGE Publications
- Published
- 2006-06
- Volume
- 13
- Issue
- 5
- Pages
- 1028-1040
- ISSN
- 1066-5277 (ISSN-L)
- 1557-8666
- OpenAlex
- W1973862547
- Cited by
- 496
- References
- 1
- FWCI
- 1.35
- Type
- journal article
- Language
- en
- Open access
- closed
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
How to cite
Cite CoChat for the checks on this page, and the paper for its own findings.
- This page
- CoChat. (2026). Citation check: A Fast and Symmetric DUST Implementation to Mask Low-Complexity DNA Sequences. https://app.cochat.ai/papers/10.1089/cmb.2006.13.1028
- The paper
- Morgulis, A., Gertz, E. M., Schäffer, A. A., & Agarwala, R. (2006). A Fast and Symmetric DUST Implementation to Mask Low-Complexity DNA Sequences. Journal of Computational Biology. https://doi.org/10.1089/cmb.2006.13.1028
Data sources
Bibliographic data: Semantic Scholar, OpenAlex, Crossref.
Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.
