The DOI matches its Crossref record; 2 of the 2 references it cites were found in a registry or an index.
Issues in bioinformatics benchmarking: the case study of multiple sequence alignment
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.
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
The source backs part of the claim, not all of it — or backs it for a different population, condition or comparison.
In the citing paper
“Research has found that benchmarks are rarely impartial and instead shaped by the environments in which the benchmarks are made”
From The Leaderboard Illusion (2025) · cites this paper as Aniba et al., 2010
Experimental — accuracy not yet measured
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
Announcing the worldwide Protein Data Bank
Berman, H., Henrick, K., & Nakamura, H. (2003) · Nature Structural & Molecular Biology · doi:10.1038/nsb1203-980 · Cited by 3,093
The Pfam protein families database
Finn, R. D., Mistry, J., Tate, J., Coggill, P., Heger, A., Pollington, J. E., Gavin, O. L., Gunasekaran, P., Ceric, G., Forslund, K., et al. (2010) · Nucleic Acids Research · doi:10.1093/nar/gkp985 · Cited by 2,694
Flagged first, then by citations
Research works printed but not linked: 68
- Klipcan, 2008, Trends in genetics : TIG, 24, 142, 10.1016/j.tig.2007.12.006 · DOI
- 1996, COMMUN. ACM, 39, 105
- 1998, IEEE COMPUTER, 31, 32
- McClure, 1994, Molecular Biology and Evolution, 11, 571
- PEARSON, 1995, Protein Science, 4, 1145, 10.1002/pro.5560040613 · DOI
- Burset, 1996, Genomics, 34, 353, 10.1006/geno.1996.0298 · DOI
- Thompson, 1999, Bioinformatics, 15, 87, 10.1093/bioinformatics/15.1.87 · DOI
- Gardner, 2005, Nucleic Acids Research, 33, 2433, 10.1093/nar/gki541 · DOI
- Wilm, 2006, 1, 19, 10.1186/1748-7188-1-19 · DOI
- 2007, Bioinformatics, 23, 2648, 10.1093/bioinformatics/btm389 · DOI
- Pollard, 2004, BMC bioinformatics [electronic resource], 5, 6, 10.1186/1471-2105-5-6 · DOI
- Kim, 2010, BMC bioinformatics [electronic resource], 11, 54, 10.1186/1471-2105-11-54 · DOI
- 2009, Proteins, 9, 217
- Kolodny, 2005, Journal of molecular biology, 346, 1173, 10.1016/j.jmb.2004.12.032 · DOI
- 2009, Nucleic Acids Research, 37, D310, 10.1093/nar/gkn877 · DOI
- Chen, 2003, Proteins, 52, 88, 10.1002/prot.10390 · DOI
- 2007, Nucleic Acids Research, 35, D232, 10.1093/nar/gkl812 · DOI
- 2009, Bioinformatics, 25, 2404, 10.1093/bioinformatics/btp397 · DOI
- Cope, 2004, Bioinformatics, 20, 323, 10.1093/bioinformatics/btg410 · DOI
- Choe, 2005, Genome biology, 6, R16, 10.1186/gb-2005-6-2-r16 · DOI
- 2009, BMC BINFORMATICS, 10, 319, 10.1186/1471-2105-10-319 · DOI
- Drelie Gelasca, 2009, BMC bioinformatics [electronic resource], 10, 368, 10.1186/1471-2105-10-368 · DOI
- 2006, CURRENT BIOINFORMATICS, 1, 95, 10.2174/157489306775330552 · DOI
- MIZUGUCHI, 1998, Protein Science, 7, 2469, 10.1002/pro.5560071126 · DOI
- 2008, Nucleic Acids Research, 36, D419, 10.1093/nar/gkm993 · DOI
- Bahr, 2001, Nucleic Acids Research, 29, 323, 10.1093/nar/29.1.323 · DOI
- Thompson, 2005, Proteins, 61, 127, 10.1002/prot.20527 · DOI
- Perrodou, 2008, BMC bioinformatics [electronic resource], 9, 213, 10.1186/1471-2105-9-213 · DOI
- Raghava, 2003, BMC bioinformatics [electronic resource], 4, 47, 10.1186/1471-2105-4-47 · DOI
- Edgar, 2004, Nucleic Acids Research, 32, 1792, 10.1093/nar/gkh340 · DOI · Paper page
- 2005, Bioinformatics, 21, 1267, 10.1093/bioinformatics/bth493 · DOI
- Subramanian, 2005, BMC bioinformatics [electronic resource], 6, 66, 10.1186/1471-2105-6-66 · DOI
- Blackshields, 2006, In silico biology, 6, 321, 10.3233/ISB-00245 · DOI
- 2010, Nucleic Acids Research, 38, 2145, 10.1093/nar/gkp1196 · DOI
- Stoye, 1998, Bioinformatics, 14, 157, 10.1093/bioinformatics/14.2.157 · DOI
- 2009, Nucleic Acids Research, 37, 1011, 10.1093/nar/gkp089 · DOI
- Shakhnovich, 2004, Journal of molecular biology, 337, 933, 10.1016/j.jmb.2004.02.009 · DOI
- Goldstein, 2008, Current opinion in structural biology, 18, 170, 10.1016/j.sbi.2008.01.006 · DOI
- Petrey, 2009, Current opinion in structural biology, 19, 363, 10.1016/j.sbi.2009.02.001 · DOI
- Valas, 2009, Current opinion in structural biology, 19, 329, 10.1016/j.sbi.2009.03.011 · DOI
- Meier, 2007, Current biology : CB, 17, 173, 10.1016/j.cub.2006.10.063 · DOI
- 2008, PNAS, 105, 5057, 10.1073/pnas.0709518105 · DOI
- Brenner, 1997, Current opinion in structural biology, 7, 369, 10.1016/S0959-440X(97)80054-1 · DOI
- 1999, Nucleic Acids Research, 27, 2682, 10.1093/nar/27.13.2682 · DOI
- Baldi, 2000, Bioinformatics, 16, 412, 10.1093/bioinformatics/16.5.412 · DOI · Paper page
- du Prel, 2009, 106, 335
- Barton, 1987, Journal of molecular biology, 198, 327, 10.1016/0022-2836(87)90316-0 · DOI
- Taylor, 1988, Journal of Molecular Evolution, 28, 161, 10.1007/BF02143508 · DOI
- 1988, 73, 237
- 1996, Nucleic Acids Research, 24, 1515, 10.1093/nar/24.8.1515 · DOI
- Gotoh, 1996, Journal of molecular biology, 264, 823, 10.1006/jmbi.1996.0679 · DOI
- Thompson, 2000, Nucleic Acids Research, 28, 2919, 10.1093/nar/28.15.2919 · DOI
- Notredame, 2000, Journal of molecular biology, 302, 205, 10.1006/jmbi.2000.4042 · DOI
- Katoh, 2002, Nucleic Acids Research, 30, 3059, 10.1093/nar/gkf436 · DOI · Paper page
- Do, 2005, Genome Research, 15, 330, 10.1101/gr.2821705 · DOI
- 2007, Bioinformatics, 23, 802, 10.1093/bioinformatics/btm017 · DOI
- O'Sullivan, 2004, Journal of molecular biology, 340, 385, 10.1016/j.jmb.2004.04.058 · DOI
- 2006, Nucleic Acids Research, 34, 4364, 10.1093/nar/gkl514 · DOI
- Chakrabarti, 2006, Nucleic Acids Research, 34, 2598, 10.1093/nar/gkl274 · DOI
- 2005, PNAS, 102, 10557, 10.1073/pnas.0409137102 · DOI
- Lee, 2002, Bioinformatics, 18, 452, 10.1093/bioinformatics/18.3.452 · DOI
- 2009, Bioinformatics, 25, 2455, 10.1093/bioinformatics/btp452 · DOI
- Dessimoz, 2010, Genome biology, 11, R37, 10.1186/gb-2010-11-4-r37 · DOI
- Cozzetto, 2005, Proteins, 58, 151, 10.1002/prot.20284 · DOI
- 2010, Bioinformatics, 26, 617, 10.1093/bioinformatics/btq008 · DOI
- 2009, Bioinformatics, 25, 406, 10.1093/bioinformatics/btn633 · DOI
- 1994, Nucleic Acids Research, 22, 4673, 10.1093/nar/22.22.4673 · DOI · Paper page
- 2007, Bioinformatics, 23, 2947, 10.1093/bioinformatics/btm404 · DOI
Cited by
Sorted by citations
A comparison of single-cell trajectory inference methods
Saelens, W., Cannoodt, R., Todorov, H., & Saeys, Y. (2019) · Nature Biotechnology · doi:10.1038/s41587-019-0071-9 · Cited by 1,670
Singh, S., Nan, Y., Wang, A., D'Souza, D., Kapoor, S., Üstün, A., Koyejo, S., Deng, Y., Longpre, S., Smith, N. A., et al. (2025) · arXiv · doi:10.48550/arxiv.2504.20879 · Cited by 108
Can We Trust AI Benchmarks? An Interdisciplinary Review of Current Issues in AI Evaluation
Eriksson, M., Purificato, E., Noroozian, A., Vinagre, J., Chaslot, G., Gomez, E., & Fernandez-Llorca, D. (2025) · arXiv · doi:10.48550/arxiv.2502.06559 · Cited by 35
Metadata
- Authors
- Aniba, M. R., Poch, O., & Thompson, J. D.
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2010-07-17
- Volume
- 38
- Issue
- 21
- Pages
- 7353-7363
- ISSN
- 0305-1048
- 1362-4962
- PMC
- PMC2995051
- Cited by
- 72
- References
- 2
- Language
- en
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