CAP3: A DNA Sequence Assembly Program
Open accessAbstract
We describe the third generation of the CAP sequence assembly program. The CAP3 program includes a number of improvements and new features. The program has a capability to clip 5' and 3' low-quality regions of reads. It uses base quality values in computation of overlaps between reads, construction of multiple sequence alignments of reads, and generation of consensus sequences. The program also uses forward-reverse constraints to correct assembly errors and link contigs. Results of CAP3 on four BAC data sets are presented. The performance of CAP3 was compared with that of PHRAP on a number of BAC data sets. PHRAP often produces longer contigs than CAP3 whereas CAP3 often produces fewer errors in consensus sequences than PHRAP. It is easier to construct scaffolds with CAP3 than with PHRAP on low-pass data with forward-reverse constraints.
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
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?
After CAP3 assembly, 68,227 contigs and 128,486 singletons with length ≥75 bp were obtained.
“Then, we reassembled these sequences by using CAP3 [26] to reduce redundancy and generate longer sequences, and obtained 68,227 contigs and 128,486 singletons with length ≥75 bp after the last CAP3 assembly.”
From Digital Gene Expression Analysis Based on Integrated De Novo Transcriptome Assembly of Sweet Potato [Ipomoea batatas (L.) Lam.] (2012) · cites this paper as [26]
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Cites
Basic local alignment search tool
Altschul, S. F., Gish, W., Miller, W., Myers, E. W., & Lipman, D. J. (1990) · Journal of Molecular Biology · doi:10.1006/jmbi.1990.9999 · Cited by 98,669 · see citing works
Base-Calling of Automated Sequencer Traces Using <i>Phred.</i> II. Error Probabilities
Ewing, B., & Green, P. (1998) · Genome Research · doi:10.1101/gr.8.3.186 · Cited by 5,439 · see citing works
Flagged first, then by citations
Research works printed but not linked: 2
- Chao, K.-M., W.R. Pearson, and W. Miller. 1992. Aligning two sequences within a specified diagonal band. Comput. Appl. Biosci. 8: 481-487.
- Pearson, W.R. and D. Lipman. 1988. Improved tools for biological sequence comparison. Proc. Natl. Acad. Sci. 85: 2444-2448.
Cited by
Sorted by citations
An Eulerian path approach to DNA fragment assembly
Pevzner, P. A., Tang, H., & Waterman, M. S. (2001) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.171285098 · Cited by 1,352 · see citing works
Dowd, S. E., Callaway, T. R., Wolcott, R. D., Sun, Y., McKeehan, T., Hagevoort, R. G., & Edrington, T. S. (2008) · BMC Microbiology · doi:10.1186/1471-2180-8-125 · Cited by 1,121 · see citing works
Landscape of Somatic Retrotransposition in Human Cancers
Lee, E., Iskow, R., Yang, L., Gokcumen, O., Haseley, P., Luquette, L. J., Lohr, J. G., Harris, C. C., Ding, L., Wilson, R. K., et al. (2012) · Science · doi:10.1126/science.1222077 · Cited by 762 · see citing works
Simion, P., Philippe, H., Baurain, D., Jager, M., Richter, D. J., Di Franco, A., Roure, B., Satoh, N., Quéinnec, É., Ereskovsky, A., et al. (2017) · Current Biology · doi:10.1016/j.cub.2017.02.031 · Cited by 518 · see citing works
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 · see citing works
Sequencing and de novo analysis of a coral larval transcriptome using 454 GSFlx
Meyer, E., Aglyamova, G. V., Wang, S., Buchanan-Carter, J., Abrego, D., Colbourne, J. K., Willis, B. L., & Matz, M. V. (2009) · BMC Genomics · doi:10.1186/1471-2164-10-219 · Cited by 479 · see citing works
Gut microbiota richness promotes its stability upon increased dietary fibre intake in healthy adults
Tap, J., Furet, J., Bensaada, M., Philippe, C., Roth, H., Rabot, S., Lakhdari, O., Lombard, V., Henrissat, B., Corthier, G., et al. (2015) · Environmental Microbiology · doi:10.1111/1462-2920.13006 · Cited by 397 · see citing works
Methylotrophic methanogenic Thermoplasmata implicated in reduced methane emissions from bovine rumen
Poulsen, M., Schwab, C., Borg Jensen, B., Engberg, R. M., Spang, A., Canibe, N., Højberg, O., Milinovich, G., Fragner, L., Schleper, C., et al. (2013) · Nature Communications · doi:10.1038/ncomms2432 · Cited by 361 · see citing works
Maintenance of ancestral complexity and non-metazoan genes in two basal cnidarians
Technau, U., Rudd, S., Maxwell, P., Gordon, P. M. K., Saina, M., Grasso, L. C., Hayward, D. C., Sensen, C. W., Saint, R., Holstein, T. W., et al. (2005) · Trends in Genetics · doi:10.1016/j.tig.2005.09.007 · Cited by 337 · see citing works
Genomic insights into the evolutionary origin of Myxozoa within Cnidaria
Chang, E. S., Neuhof, M., Rubinstein, N. D., Diamant, A., Philippe, H., Huchon, D., & Cartwright, P. (2015) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1511468112 · Cited by 262 · see citing works
Comparing de novo assemblers for 454 transcriptome data
Kumar, S., & Blaxter, M. L. (2010) · BMC Genomics · doi:10.1186/1471-2164-11-571 · Cited by 255 · see citing works
Global characterization of Artemisia annua glandular trichome transcriptome using 454 pyrosequencing
Wang, W., Wang, Y., Zhang, Q., Qi, Y., & Guo, D. (2009) · BMC Genomics · doi:10.1186/1471-2164-10-465 · Cited by 224 · see citing works
De novo assembly of short sequence reads
Paszkiewicz, K., & Studholme, D. J. (2010) · Briefings in Bioinformatics · doi:10.1093/bib/bbq020 · Cited by 204 · see citing works
Tao, X., Gu, Y.-H., Wang, H.-Y., Zheng, W., Li, X., Zhao, C.-W., & Zhang, Y.-Z. (2012) · PLoS ONE · doi:10.1371/journal.pone.0036234 · Cited by 168 · see citing works
Biochemical Diversification through Foreign Gene Expression in Bdelloid Rotifers
Boschetti, C., Carr, A., Crisp, A., Eyres, I., Wang-Koh, Y., Lubzens, E., Barraclough, T. G., Micklem, G., & Tunnacliffe, A. (2012) · PLoS Genetics · doi:10.1371/journal.pgen.1003035 · Cited by 171 · see citing works
The neuropeptide complement of the marine annelid Platynereis dumerilii
Conzelmann, M., Williams, E. A., Krug, K., Franz-Wachtel, M., Macek, B., & Jékely, G. (2013) · BMC Genomics · doi:10.1186/1471-2164-14-906 · Cited by 165 · see citing works
Huvet, A., Herpin, A., Dégremont, L., Labreuche, Y., Samain, J.-F., & Cunningham, C. (2004) · Gene · doi:10.1016/j.gene.2004.09.008 · Cited by 158 · see citing works
Corominas, R., Yang, X., Lin, G. N., Kang, S., Shen, Y., Ghamsari, L., Broly, M., Rodriguez, M., Tam, S., Wanamaker, S. A., et al. (2014) · Nature Communications · doi:10.1038/ncomms4650 · Cited by 140 · see citing works
Manmathan, H., Shaner, D., Snelling, J., Tisserat, N., & Lapitan, N. (2013) · Journal of Experimental Botany · doi:10.1093/jxb/ert003 · Cited by 99 · see citing works
Scorrano, S., Aglieri, G., Boero, F., Dawson, M. N., & Piraino, S. (2016) · Zoological Journal of the Linnean Society · doi:10.1111/zoj.12494 · Cited by 95 · see citing works
New genomic data and analyses challenge the traditional vision of animal epithelium evolution
Belahbib, H., Renard, E., Santini, S., Jourda, C., Claverie, J.-M., Borchiellini, C., & Le Bivic, A. (2018) · BMC Genomics · doi:10.1186/s12864-018-4715-9 · Cited by 71 · see citing works
On the phylogenetic position of Myzostomida: Can 77 genes get it wrong?
Bleidorn, C., Podsiadlowski, L., Zhong, M., Eeckhaut, I., Hartmann, S., Halanych, K. M., & Tiedemann, R. (2009) · BMC Evolutionary Biology · doi:10.1186/1471-2148-9-150 · Cited by 59 · see citing works
Novel point mutations in the ERG11 gene in clinical isolates of azole resistant Candida species
Silva, D. B. D. S., Rodrigues, L. M. C., Almeida, A. A. D., Oliveira, K. M. P. D., & Grisolia/, A. B. (2016) · Memórias do Instituto Oswaldo Cruz · doi:10.1590/0074-02760150400 · Cited by 42 · see citing works
Yang, H., Hu, L., Hurek, T., & Reinhold-Hurek, B. (2010) · BMC Genomics · doi:10.1186/1471-2164-11-705 · Cited by 42 · see citing works
Identification of Key Functional Residues in the Active Site of Human β1,4-Galactosyltransferase 7
Talhaoui, I., Bui, C., Oriol, R., Mulliert, G., Gulberti, S., Netter, P., Coughtrie, M. W. H., Ouzzine, M., & Fournel-Gigleux, S. (2010) · Journal of Biological Chemistry · doi:10.1074/jbc.m110.151951 · Cited by 26 · see citing works
- Authors
- Huang, X., & Madan, A.
- Affiliations
- Michigan Technological University (US)
- Corresponding author
- Huang, Xiaoqiu
- Venue
- Genome Research
- Publisher
- Cold Spring Harbor Laboratory
- Published
- 1999-09-01
- Volume
- 9
- Issue
- 9
- Pages
- 868-877
- ISSN
- 1088-9051 (ISSN-L)
- 1549-5469
- PMC
- PMC310812
- OpenAlex
- W2166265186
- Cited by
- 5,261
- References
- 2
- Citations by year
- 2026: 65 · 2025: 80 · 2024: 101 · 2023: 131 · 2022: 135 · 2021: 194 · 2020: 214 · 2019: 228 · 2018: 206 · 2017: 261 · 2016: 278 · 2015: 311 · 2014: 339 · 2013: 348 · 2012: 360
- Type
- posted content
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- Genome Research (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Iowa State University Digital Repository (Iowa State University) (submittedVersion)
- Digital Commons - Michigan Tech (Michigan Technological University) (submittedVersion)
- Funders
- National Institutes of Health (5r01hg001502-07)
- National Human Genome Research Institute (R01 HG01502-03)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Physical Sciences › Computer Science › Artificial Intelligence › Algorithms and Data Compression
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Fractal and DNA sequence analysis
- Keywords
- CAP3, DNA sequence assembly, BAC sequencing, consensus sequence, low-pass sequencing
- MeSH terms
- Algorithms, Chromosomes, Bacterial, Models, Genetic, Models, Theoretical, Software, Reproducibility of Results, Databases, Factual, Consensus Sequence, Sequence Alignment, Sequence Analysis, DNA, Contig Mapping
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
