CAP3 protocols

CAP3 computational protocol

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 IN pipelines

PMCID: 5407641
PMID: 28448540
DOI: 10.1371/journal.pone.0176337

[…] from ests using vecscreen and estclean tool of ncbi. a summary of unigene statistics has been illustrated in table 1. trimming resulted in 244 good quality sequences which were assembled using cap3 [17] program into 134 non-redundant unigene sequences. of these, 106 were singletons whereas the remaining was assembled into 28 contigs. the unigene length ranged from 102–1156 base pair (bp) […]

PMCID: 5407641
PMID: 28448540
DOI: 10.1371/journal.pone.0176337

[…] tool ( low quality and short sequences were removed. high quality ests were assembled into contigs and singleton using the contig assembly program, cap3 following default parameters. gene ontology (go) annotation of unigenes was performed using blast2gopro ( sequences were annotated using blastx […]

PMCID: 5479533
PMID: 28636618
DOI: 10.1371/journal.pone.0179083

[…] and the longest sequence of 15,030 bp. these contigs were further assembled into 94,580 scaffolds (average length = 850 bp) with n50 = 1,179 bp. after clustering to other animals, using the software cap3 est [21], 81,185 unigenes (scaffolds that cannot be extended on either end) with a mean length of 905 bp (contig n50 = 2,992 bp) (s3 table) were generated, comprising 73,440,746 bp in total. […]

PMCID: 5534050
PMID: 28754134
DOI: 10.1186/s12985-017-0810-9

[…] in florida include 32 plants (16 clones) of former commercial sugarcane varieties maintained in commercial field environment, following de novo contig assembly of cleaned reads performed using cap3 [14] and searches using blastn (basic local alignment search tool) and blastx [15], 34 contigs with detectable homology to mastreviruses were identified from nine of these 717 plant samples […]

PMCID: 5603166
PMID: 28922359
DOI: 10.1371/journal.pone.0184319

[…] scientific, waltham, ma)., the national center for biotechnology information (ncbi) o. basilicum expressed sequence tag (est) database of 23,845 cdna sequences was downloaded and assembled using cap3 software [42] with default settings. the resulting contig and remaining singlet sequences were mined with sciroko software [43] for di-, tri- and tetranucleotide repeat sequences with a minimum […]

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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