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PORTRAIT specifications

Information


Unique identifier OMICS_05863
Name PORTRAIT
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

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Information


Unique identifier OMICS_05863
Name PORTRAIT
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Publication for PORTRAIT

PORTRAIT citations

 (11)
library_books

Characterization and analysis of long non coding rna (lncRNA) in In Vitro and Ex Vivo derived cardiac progenitor cells

2017
PLoS One
PMCID: 5481004
PMID: 28640894
DOI: 10.1371/journal.pone.0180096

[…] ose genes in the d8 /CLK CPC samples.The use of bioinformatics analysis tools that are tailored for screening sequencing data for identifiable features unique to lncRNA genes, such as PhyloCSF [] and PORTRAIT [], was beyond the scope of our expertise. Instead, we sought to identify putative lncRNA genes based on their lack of inclusion in the most current mouse genome build, mm10. That is, any uni […]

library_books

Identification and functional analysis of long intergenic noncoding RNA genes in porcine pre implantation embryonic development

2016
Sci Rep
PMCID: 5138625
PMID: 27922056
DOI: 10.1038/srep38333

[…] o-expression network and investigated the hub lincRNAs that may be likely to be key in driving porcine PED.During the past 5 years, several tools heavily relied on sequence alignment, such as CPC and PORTRAIT, have been developed to predict the coding potential based on known protein database. However, most lincRNA discovered tend to be lineage specific and less conserved. For example, only 993 of […]

library_books

The Tetraodon nigroviridis reference transcriptome: developmental transition, length retention and microsynteny of long non coding RNAs in a compact vertebrate genome

2016
Sci Rep
PMCID: 5024134
PMID: 27628538
DOI: 10.1038/srep33210

[…] than the mean NCP score of all potential lncRNAs (0.76) was used to call the final lncRNA set while the remaining transcripts were placed within coding class. It is worth noticing that Annocript uses Portrait to generate the NCP score. According to Portrait authors, a non-coding potential score bigger than 0.5 is sufficient to classify a transcript as non-coding. We applied more stringent conditio […]

library_books

De novo assembly and sex specific transcriptome profiling in the sand fly Phlebotomus perniciosus (Diptera, Phlebotominae), a major Old World vector of Leishmania infantum

2015
BMC Genomics
PMCID: 4619268
PMID: 26493315
DOI: 10.1186/s12864-015-2088-x

[…] The prediction of coding potential of transcripts not annotated in the PERNI data set was performed, as described in Salvemini et al., 2014 [], using three independent prediction methods: the Portrait software (performed in this paper as a plugin within the Annocript pipeline) [, ], the Coding Potential Calculator (CPC) [] and the Coding Potential Assessment Tool (CPAT) []. In order to ide […]

library_books

Inferring bona fide transfrags in RNA Seq derived transcriptome assemblies of non model organisms

2015
BMC Bioinformatics
PMCID: 4344733
PMID: 25880035
DOI: 10.1186/s12859-015-0492-5

[…] Assembled transcripts were evaluated for protein-coding attributes using PORTRAIT []. We corrected PORTRAIT to run ANGLE [] in 6 frames, since the biological orientation of transfrags from non-strand specific libraries cannot be readily ascertained. The predicted open read […]

library_books

De Novo Assembly and Transcriptome Analysis of the Mediterranean Fruit Fly Ceratitis capitata Early Embryos

2014
PLoS One
PMCID: 4256415
PMID: 25474564
DOI: 10.1371/journal.pone.0114191

[…] a reference. In CPC a positive coding potential score indicates a protein coding potential of the respective target transcript, whereas negative values predict non-coding potential of transcripts. In Portrait the coding and non-coding potential of transcripts are expressed in percentage while in CPAT the coding probability score ranges between 0 and 1 with coding probability cut-off usually set at […]

Citations

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PORTRAIT institution(s)
Biology Institute, University of Brasília, Brazil

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