polyadq protocols

View polyadq computational protocol

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polyadq specifications

Information


Unique identifier OMICS_06162
Name polyadq
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Taxon


  • Primates
    • Homo sapiens

Publication for polyadq

polyadq in pipelines

 (2)
2011
PMCID: 3113978
PMID: 21535884
DOI: 10.1186/1743-422X-8-200

[…] by detecting the promoter http://www.fruitfly.org/seq_tools/promoter.html[], and the presence of tata box http://motif.genome.jp/ and transcription terminal signals http://rulai.cshl.org/tools/polyadq/polyadq_form.html. searches of the deduced proteins for signal peptides http://www.cbs.dtu.dk/services/signalp/, transmembrane regions http://www.ch.embnet.org/software/tmpred_form.html, […]

2009
PMCID: 3032949
PMID: 21637656
DOI: 10.1590/S1415-47572009005000003

[…] transcription start sites (tss). the core promoters found in this search were examined for the presence of tata box sequences using the transfacfind search engine (http://motif.genome.jp/)., polyadq, a eukaryotic polyadenylation (poly a) signal search engine (cold spring harbor laboratory, http://rulai.cshl.org/tools/polyadq/polyadq_form.html) was used to predict transcription […]


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polyadq in publications

 (17)
PMCID: 5854547
DOI: 10.1016/j.omtn.2018.01.011

[…] of new regulatory mechanisms into the transcript that negatively impact on protein expression., in silico analysis of the extended 3′ utr was carried out using the online tools utrscan, mirbase, polyadq, and dna functional site miner (dna fs miner). lists the potential regulatory elements identified within intron 7 from each of these databases, and a illustrates the location […]

PMCID: 5673974
PMID: 29109480
DOI: 10.1038/s41598-017-15076-3

[…] either the 6th or the 9th polyadenylation signal instead of the canonical polyadenylation signal (fig. , supplementary table ). preference for the 9th polyadenylation signal is in agreement with polyadq prediction (supplementary table ), a web-based polyadenylation signal prediction tool. however, the 6th polyadenylation signal was defined as a false signal by polyadq, even though […]

PMCID: 3388047
PMID: 22768332
DOI: 10.1371/journal.pone.0040098

[…] codon. only those 3′utr sequences which already included a poly(a) tail or contained at least one poly(a) site downstream of the initial orf termination codon, as determined by scanning with the polyadq program or manually for non-canonical poly(a) signals, were considered for further study., table listing all potential utrs identified through available online databases., the majority […]

PMCID: 3346806
PMID: 22586462
DOI: 10.1371/journal.pone.0036151

[…] analysed in detail for conservation across different species. in addition, we checked exon organization, chromosomal location and proximity to known chemokine genes, presence of a polya sites and polyadq, transcription factor binding sites of chemokine regulators and gene expression profiles. their protein sequences were analysed for glycosylation sites and subcellular localization (for […]

PMCID: 3329446
PMID: 22530027
DOI: 10.1371/journal.pone.0035461

[…] poly(a) signals (one aauaaa hexamer, two auuaaa hexamers, and one gauaaa hexamer) can be recognized for its 3′-end cleavage and polyadenylation. these results confirm those obtained when we used the polyadq program (http://rulai.cshl.org/tools/polyadq/polyadq_form.html) to evaluate potential poly(a) signals in the human hfe 3′ utr – this program predicted that the aauaaa and auuaaa sites […]


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polyadq institution(s)
Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA

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