CAP3: A DNA Sequence Assembly Program. 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.

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  1. Tsakiris, Manolis C.; Peng, Liangzu; Conca, Aldo; Kneip, Laurent; Shi, Yuanming; Choi, Hayoung: An algebraic-geometric approach for linear regression without correspondences (2020)
  2. Wright, Christopher; Krishnamoorty, Sriram; Kulkarni, Milind: MULKSG: \textitMULtiple\textitK\textitSimultaneous\textitGraphassembly (2019)
  3. Axelson-Fisk, Marina: Comparative gene finding. Models, algorithms and implementation (2015)
  4. Indumathy, R.; Maheswari, S. Uma; Subashini, G.: Nature-inspired novel Cuckoo search algorithm for genome sequence assembly (2015)
  5. Blazewicz, Jacek; Frohmberg, Wojciech; Gawron, Piotr; Kasprzak, Marta; Kierzynka, Michal; Swiercz, Aleksandra; Wojciechowski, Pawel: DNA sequence assembly involving an acyclic graph model (2013)
  6. Jones, Martin O.; Koutsovoulos, Georgios D.; Blaxter, Mark L.: Iphy: an integrated phylogenetic workbench for supermatrix analyses (2011) ioport
  7. Prosperi, Mattia C. F.; Prosperi, Luciano; Bruselles, Alessandro; Abbate, Isabella; Rozera, Gabriella; Vincenti, Donatella; Solmone, Maria Carmela; Capobianchi, Maria Rosaria; Ulivi, Giovanni: Combinatorial analysis and algorithms for quasispecies reconstruction using next-generation sequencing (2011) ioport
  8. Liang, Chunguang; Schmid, Alexander; López-Sánchez, María José; Moya, Andres; Gross, Roy; Bernhardt, Jörg; Dandekar, Thomas: JANE: efficient mapping of prokaryotic ests and variable length sequence reads on related template genomes (2009) ioport
  9. Nasser, Sara; Breland, Adrienne; Harris, Frederick C.; Nicolescu, Monica; Vert, Gregory L.: Fuzzy genome sequence assembly for single and environmental genomes (2009)
  10. Papanicolaou, Alexie; Stierli, Remo; Ffrench-Constant, Richard H.; Heckel, David G.: Next generation transcriptomes for next generation genomes using \textitest2assembly (2009) ioport
  11. Picardi, Ernesto; Mignone, Flavio; Pesole, Graziano: Easycluster: a fast and efficient gene-oriented clustering tool for large-scale transcriptome data (2009) ioport
  12. Minetti, Gabriela; Alba, Enrique; Luque, Gabriel: Seeding strategies and recombination operators for solving the DNA fragment assembly problem (2008)
  13. Nebro, A. J.; Luque, G.; Luna, F.; Alba, E.: DNA fragment assembly using a grid-based genetic algorithm (2008)
  14. Givan, Scott A.; Sullivan, Christopher M.; Carrington, James C.: The personal sequence database: a suite of tools to create and maintain web-accessible sequence databases (2007) ioport
  15. Deonier, Richard C.; Tavaré, Simon; Waterman, Michael S.: Computational genome analysis. An introduction. (2005)
  16. Wang, Jason T. L.; Zaki, Mohammed J.; Toivonen, Hannu T. T.; Shasha, Dennis: Data mining in bioinformatics (2005)
  17. Pevzner, Pavel A.; Tang, Haixu; Waterman, Michael S.: An Eulerian path approach to DNA fragment assembly (2001)