The DOI matches its Crossref record; 2 of the 2 references it cites were found in a registry or an index.
ProbCons: Probabilistic consistency-based multiple sequence alignment
Open accessAbstract
To study gene evolution across a wide range of organisms, biologists need accurate tools for multiple sequence alignment of protein families. Obtaining accurate alignments, however, is a difficult computational problem because of not only the high computational cost but also the lack of proper objective functions for measuring alignment quality. In this paper, we introduce probabilistic consistency , a novel scoring function for multiple sequence comparisons. We present ProbCons, a practical tool for progressive protein multiple sequence alignment based on probabilistic consistency, and evaluate its performance on several standard alignment benchmark data sets. On the BAliBASE, SABmark, and PREFAB benchmark alignment databases, ProbCons achieves statistically significant improvement over other leading methods while maintaining practical speed. ProbCons is publicly available as a Web resource.
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
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
Needleman, S. B., & Wunsch, C. D. (1970) · Journal of Molecular Biology · doi:10.1016/0022-2836(70)90057-4 · Cited by 11,288
Cited by
progressiveMauve: Multiple Genome Alignment with Gene Gain, Loss and Rearrangement
Darling, A. E., Mau, B., & Perna, N. T. (2010) · PLoS ONE · doi:10.1371/journal.pone.0011147 · Cited by 3,848
Sela, I., Ashkenazy, H., Katoh, K., & Pupko, T. (2015) · Nucleic Acids Research · doi:10.1093/nar/gkv318 · Cited by 835
Phylogenetic tree building in the genomic age
Kapli, P., Yang, Z., & Telford, M. J. (2020) · Nature Reviews Genetics · doi:10.1038/s41576-020-0233-0 · Cited by 533
Alignment Uncertainty and Genomic Analysis
Wong, K. M., Suchard, M. A., & Huelsenbeck, J. P. (2008) · Science · doi:10.1126/science.1151532 · Cited by 411
Auxin-related gene families in abiotic stress response in Sorghum bicolor
Wang, S., Bai, Y., Shen, C., Wu, Y., Zhang, S., Jiang, D., Guilfoyle, T. J., Chen, M., & Qi, Y. (2010) · Functional & Integrative Genomics · doi:10.1007/s10142-010-0174-3 · Cited by 297
Thompson, J. D., Linard, B., Lecompte, O., & Poch, O. (2011) · PLoS ONE · doi:10.1371/journal.pone.0018093 · Cited by 242
A formal test of the theory of universal common ancestry
Theobald, D. L. (2010) · Nature · doi:10.1038/nature09014 · Cited by 231
Multiple sequence alignment modeling: Methods and applications
Chatzou, M., Magis, C., Chang, J.-M., Kemena, C., Bussotti, G., Erb, I., & Notredame, C. (2016) · Briefings in Bioinformatics · doi:10.1093/bib/bbv099 · Cited by 229
Dynamically evolving novel overlapping gene as a factor in the SARS-CoV-2 pandemic
Nelson, C. W., Ardern, Z., Goldberg, T. L., Meng, C., Kuo, C.-H., Ludwig, C., Kolokotronis, S.-O., & Wei, X. (2020) · eLife · doi:10.7554/elife.59633 · Cited by 87
Issues in bioinformatics benchmarking: the case study of multiple sequence alignment
Aniba, M. R., Poch, O., & Thompson, J. D. (2010) · Nucleic Acids Research · doi:10.1093/nar/gkq625 · Cited by 72
New substitution models for rooting phylogenetic trees
Williams, T. A., Heaps, S. E., Cherlin, S., Nye, T. M. W., Boys, R. J., & Embley, T. M. (2015) · Philosophical Transactions of the Royal Society B: Biological Sciences · doi:10.1098/rstb.2014.0336 · Cited by 61
“Sequences were aligned with MUSCLE [46], MAFFT [47], P ROB C ONS [48] and K ALIGN [49], and a consensus alignment inferred using M-C OFFEE [50].”
Evaluating the Accuracy and Efficiency of Multiple Sequence Alignment Methods
Pervez, M. T., Babar, M. E., Nadeem, A., Aslam, M., Awan, A. R., Aslam, N., Hussain, T., Naveed, N., Qadri, S., Waheed, U., et al. (2014) · Evolutionary Bioinformatics · doi:10.4137/ebo.s19199 · Cited by 48
Xie, R., Zan, X., Chu, L., Su, Y., Xu, P., & Liu, W. (2023) · BMC Bioinformatics · doi:10.1186/s12859-023-05237-9 · Cited by 32
Lukács, G., Papp, T., Somogyvári, F., Csernetics, Á., Nyilasi, I., & Vágvölgyi, C. (2009) · Antonie van Leeuwenhoek · doi:10.1007/s10482-008-9287-2 · Cited by 19
Nahas, J. V., Iosue, C. L., Shaik, N. F., Selhorst, K., He, B. Z., & Wykoff, D. D. (2018) · G3 Genes Genomes Genetics · doi:10.1534/g3.118.200303 · Cited by 8
McWhite, C. D., & Singh, M. (2022) · doi:10.1101/2022.10.21.513099 · Cited by 4
Metadata
- Authors
- Do, C. B., Mahabhashyam, M. S. P., Brudno, M., & Batzoglou, S.
- Venue
- Genome Research
- Publisher
- Cold Spring Harbor Laboratory
- Published
- 2005-02
- Volume
- 15
- Issue
- 2
- Pages
- 330-340
- ISSN
- 1088-9051 (ISSN-L)
- OpenAlex
- W2140872496
- Cited by
- 1,114
- References
- 2
- Type
- posted content
- Language
- en
- Open access
- hybrid
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
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.
