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This form allows you to assemble a set of contiguous sequences (contigs) with the CAP3 program. If you use CAP3 in any published work, please cite the following reference: Huang, X. and Madan, A. (1999) CAP3: A DNA sequence assembly program.
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The PRABI-Doua is devoted to bioinformatics tools available...
- Software and Packages
1 Σεπ 1999 · CAP3: A DNA sequence assembly program. The third generation of the CAP sequence assembly program is described, which has a capability to clip 5' and 3' low-quality regions of reads and uses forward-reverse constraints to correct assembly errors and link contigs. PCAP: a whole-genome assembly program.
File Formats Used at PRABI-Doua FASTA format. A sequence in FASTA format begins with a single-line description, followed by lines of sequence data. The description line is distinguished from the sequence data by a greater-than ('>') symbol in the first column. It is recommended that all lines of text be shorter than 80 characters in length ...
CAP3 makes use of a large number of forward-reverse constraints to locate and correct errors in layout of sequence reads. This capability allows CAP3 to address assembly errors due to repeats. CAP3 also uses constraints to link contigs separated by a gap. This feature provides useful information to sequence finishers.
3 Μαΐ 2018 · Often sequence assembly programs such as CAP3 [cap] and Phrap [phrap] are used. Sequence assemblies are either contigs whose sequences correspond to the consensus sequences of the alignments or singletons that are not similar to other ESTs and, therefore, cannot be grouped into contigs .
CpGProD is a program dedicated to the prediction of promoters associated with CpG islands (CGIs) in mammalian genomic sequences. CpGProD is available either via a web server, useful for a small dataset, or as a standalone application for a larger dataset (see below).
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