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.

CAP3 article

CAP3 citations

PMCID: 5751311

[…] clean paired-end reads (table 1). unigenes were then de novo assembled using trinity [55] through all of the seven rna-seq samples in the wild-type ji2822 background, respectively. we then used cap3 to further assemble overlapping regions from a pool of all contigs from each of the rna-seq assemblies [56]. the resulting cap3 contigs and singlets were combined together […]

PMCID: 5702389

[…] clean reads were used for the subsequent analysis., all the clean reads from the mono- and co-culture systems were pooled and assembled using the trinity assembly algorithm for primary unigene and cap3 est for final unigene (first_contig and second_contig) (huang and madan, 1999; grabherr et al., 2011). the acquired final unigene sequences were searched against the ncbi non-redundant (nr) […]

PMCID: 5702422

[…] low quality sequences, ests with less than 100 bp and more than 800 bp were discarded and clipped at 3′ end (thiel et al., 2003). the processed and filtered sequences were then assembled using cap3 (huang and madan, 1999) program. transcriptome data encompassing 2,148,658 and 933,376 transcript sequences respectively from gse73201and gse66389, 799 assembled ests, 2774 ests singleton […]

PMCID: 5479533

[…] 20 nucleotides, and ribosome rna reads were removed. the remaining clean reads were firstly assembled using clc genomics workbench to obtain the primary unigenes, which were then assembled using cap3 est [21] to obtain the final unigenes of real animals, as described for de novo transcriptome assemblies without a reference genome. the quality of the assembly was critically assessed by sbc […]

PMCID: 5407641

[…] 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) […]

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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