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PORTRAIT specifications

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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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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 in publications

 (6)
PMCID: 4619268
PMID: 26493315
DOI: 10.1186/s12864-015-2088-x

[…] and l. longipalpis transcriptomes (additional file : table s4).fig. 3, the annocript annotation pipeline performs also a prediction of the putative long non-coding rnas (lncrnas) through the portrait software, which uses support vector machine and is optimized for non-model organisms []. in brief, a transcript is annotated as non-coding if it has (i) no match in public databases, (ii) […]

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

[…] -p 1 (substring removal, +/+). in addition, we evaluated the redundancy in each assembly using cd-hit-est as describe by []., 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 […]

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

[…] non-annotated unigenes) to search for putative long non-coding transcripts. we used three different applications: the coding potential calculator (cpc, ), which uses machine-learning methods; the portrait tool , which uses support vector machine and is optimized for non-model organisms; and the alignment-independent coding potential assessment tool, which uses logistic regression . to ensure […]

PMCID: 4223053
PMID: 25375103
DOI: 10.1371/journal.pone.0112420

[…] matched against those data sets were searched by blastx against the uniref100 protein sequences downloaded from uniprot . for all contigs, orfs were identified and coding potential assessed using portrait v. 1.1 . since the portrait score for coding potential is strand-specific, we retained the higher of the two scores for forward and reverse-complement sequences. translated orfs […]

PMCID: 4122929
PMID: 24951567
DOI: 10.1093/gbe/evu131

[…] (paralog pairs, c1, and c2) were tested for using kruskal–wallis and mann–whitney tests., to further test for potential functional changes, we estimated the coding potential for each sequence using portrait (). a portrait score of less than 0.5 indicates a low probability of that the sequence codes for a protein, and a portrait score greater than 0.5 indicates a high probability […]


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

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