PolyA_SVM statistics

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Associated diseases

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PolyA_SVM specifications

Information


Unique identifier OMICS_06160
Name PolyA_SVM
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Perl
Computer skills Advanced
Stability Stable
Maintained Yes

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Information


Unique identifier OMICS_06160
Name PolyA_SVM
Interface Web user interface
Restrictions to use None
Programming languages Perl
Computer skills Basic
Stability Stable
Maintained Yes

Publication for PolyA_SVM

PolyA_SVM in publications

 (7)
PMCID: 4878157
PMID: 27174320
DOI: 10.4103/0366-6999.181965

[…] resistant to chemotherapy, metastatic dissemination, tumor recurrence, and poor prognosis.[] like hmga2, survivin mrna has a long 3'-utr of 2100 nt with nine putative apa sites as predicted by polya_svm software (http://exon.umdnj.edu/polya_svm_server/index.html) and nearly 40 mirna target sites as predicted by targetscan software (www.targetscan.org). although transcriptional reactivation […]

PMCID: 3688553
PMID: 23818875
DOI: 10.1371/journal.pgen.1003594

[…] the overlap intervals tool in galaxy (version 1.0.0)., intersection of snps with validated and predicted polyadenylation sites was performed using annotation in the polya-db database (polya_db 1 and polya_svm) on ucsc (table browser tool). detection of snps within polyadenylation signals was performed by extracting the strand specific sequence five nucleotide upstream and downstream each snp […]

PMCID: 3549828
PMID: 23368518
DOI: 10.1186/1471-2105-14-S2-S9

[…] accuracy was reported as the average of twenty ten-fold cross validations. linear discriminant analysis (lda) and logistic regression (lr) were performed by python machine learning package mlpy []., polya_svm [] version 2.1 was downloaded from http://exon.umdnj.edu/polya_svm/, and polya-ep [] was downloaded from http://mlkd.csd.auth.gr/polya/tools.html. polya_svm was tested on 22,479 human […]

PMCID: 3118111
PMID: 21569433
DOI: 10.1186/1472-6750-11-51

[…] mrnas with ires-like activity that increases translation []. the 5'-utr of cho s100a6 gene was therefore searched by a web-based ires secondary structure prediction tool []http://polya.umdnj.edu/polya_svm, but no ires-like structure could be predicted, whereas three potential cap-independent translation initiation sites where found in the 5'-utr of the human cirp gene (genbank: d78134) […]

PMCID: 2935562
PMID: 20819935
DOI: 10.1083/jcb.201002043

[…] both human genes contain a sequence matching the translation initiation start site consensus (underline) for vertebrates (gccgccaccauggcg; ; ), and depending on the search program used (“polyadq” or polya_svm program), h3.x and h3.y 3′ genomic sequences of human and primate origins were predicted to include a conserved poly-a site (; ). alignment of human and primate h3.x and h3.y coding […]


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PolyA_SVM institution(s)
Department of Mathematical Sciences, New Jersey Institute of Technology Newark, NJ, USA

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