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CAP3 specifications


Unique identifier OMICS_12802
Name CAP3
Interface Web user interface
Restrictions to use None
Input format FASTA
Computer skills Basic
Version 3.0
Maintained No


This tool is not maintained anymore.

Publication for CAP3

CAP3 citations


The aquatic animals’ transcriptome resource for comparative functional analysis

BMC Genomics
PMCID: 5954267
PMID: 29764375
DOI: 10.1186/s12864-018-4463-x

[…] h default parameters. After the first step assembly in three assembler, we selected high read coverage and relatively long length as the representative transcript and conducted further assembly using CAP3 Version Date: 2007–10-15 [] with an overlap length cutoff of 200 and overlap percent identity cutoff of 99 (−o 200 -p 99) []. To obtain comprehensive transcriptomes from various assemblers [, ], […]


Identifying Group Specific Sequences for Microbial Communities Using Long k mer Sequence Signatures

Front Microbiol
PMCID: 5943621
PMID: 29774017
DOI: 10.3389/fmicb.2018.00872

[…] The identified group-specific 40-mers were assembled into group-specific sequences using CAP3 (), in which 11 assembled sequences were longer than 200 bp, with length from 210 to 350 bp (available in Supplementary File ). They were aligned by the sequencing reads from the training and val […]


Sialome diversity of ticks revealed by RNAseq of single tick salivary glands

PLoS Negl Trop Dis
PMCID: 5919021
PMID: 29652888
DOI: 10.1371/journal.pntd.0006410

[…] bed previously using the assemblers Abyss and Soapdenovo-Trans with every kmer ending in 1 and 5 (-k program switch) from 21 to 95 [–]. Resulting contigs were re-assembled by a pipeline of blastn and cap3 assembler [] as described earlier []. Coding sequences were extracted based on blastx [] results deriving from several database matches, including a subset of the non-redundant protein database o […]


Molecular mechanisms of fission in echinoderms: Transcriptome analysis

PLoS One
PMCID: 5897022
PMID: 29649336
DOI: 10.1371/journal.pone.0195836

[…] tracting non-metionin started CDS. Then, all CDS was clustered CD-HIT 4.6 [,] with the following parameters “-n 7 -c 0.9 -G 0 -aS 0.8 -A 120” and overassembled using the own Python script ThreadHomoloCAP3. For assembly of sequences with small (> 30 nt) end overlaps, CAP3 were used with “-r 0 -p 95 -o 30 -h 3 -y 10 -t 500 -s 400 -i 32 -j 42” parameters []. Then, a SPAdes part “corrector” was used f […]


PCR RFLP assay as an option for primary HPV test

Braz J Med Biol Res
PMCID: 5886552
PMID: 29590262
DOI: 10.1590/1414-431X20177098
call_split See protocol

[…] e manufacturers' instructions. Automated DNA sequencing was performed in an ABI 3730 Genetic Analyzer sequencer (Applied Biosystems, USA). The accuracy of the DNA sequencing was evaluated through the CAP3 program based on Phred quality score ().Sequences were aligned and compared to those available in the GenBank database using the software Chromas Lite 2.1 (Technelysium, Australia). HPV type was […]


The mRNA and miRNA transcriptomic landscape of Panax ginseng under the high ambient temperature

BMC Syst Biol
PMCID: 5861484
PMID: 29560829
DOI: 10.1186/s12918-018-0548-z

[…] a sets, we used the Trinity in silico normalization. All parameters were set as default. As a result 62.9 million base pairs and 744,507 contigs were assembled. We further performed scaffolding using CAP3 [] to acquire a total of 613,448 scaffolded contigs. To compensate for sequence variations caused by sub-species difference, our transcriptome RNA-seq reads were used to build sample specific con […]


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CAP3 institution(s)
Department of Computer Science, Michigan Technological University, Houghton, MI, USA; Department of Molecular Biotechnology, University of Washington, School of Medicine, Seattle, WA, USA
CAP3 funding source(s)
National Institutes of Health grant R01 HG01502-03

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