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.
Keywords for this software
References in zbMATH (referenced in 6 articles )
Showing results 1 to 6 of 6.
- Indumathy, R.; Maheswari, S.Uma; Subashini, G.: Nature-inspired novel Cuckoo search algorithm for genome sequence assembly (2015)
- Blazewicz, Jacek; Frohmberg, Wojciech; Gawron, Piotr; Kasprzak, Marta; Kierzynka, Michal; Swiercz, Aleksandra; Wojciechowski, Pawel: DNA sequence assembly involving an acyclic graph model (2013)
- Nasser, Sara; Breland, Adrienne; Harris, Frederick C.; Nicolescu, Monica; Vert, Gregory L.: Fuzzy genome sequence assembly for single and environmental genomes (2009)
- Minetti, Gabriela; Alba, Enrique; Luque, Gabriel: Seeding strategies and recombination operators for solving the DNA fragment assembly problem (2008)
- Nebro, A.J.; Luque, G.; Luna, F.; Alba, E.: DNA fragment assembly using a grid-based genetic algorithm (2008)
- Pevzner, Pavel A.; Tang, Haixu; Waterman, Michael S.: An Eulerian path approach to DNA fragment assembly (2001)