PlantPAN protocols

PlantPAN specifications

Information


Unique identifier OMICS_09582
Name PlantPAN
Alternative name Plant Promoter Analysis Navigator
Interface Web user interface
Restrictions to use None
Computer skills Basic
Version 2.0
Stability Stable
Maintained Yes

Maintainer


  • person_outline Wen-Chi Chang <>

Publications for Plant Promoter Analysis Navigator

PlantPAN IN pipelines

 (5)
2018
PMCID: 5920332
PMID: 29514290
DOI: 10.1093/jxb/ery083

[…] elements present in at least three different species, including sugarcane, were considered in the search for putative transcription factor binding sites (tfbs). we identified putative tfbs using the plantpan 2.0 database (chow et al., 2016), and the resulting cis-element sequences were manually double-checked against original references; elements containing inconsistencies were discarded., yeast […]

2017
PMCID: 5539077
PMID: 28824677
DOI: 10.3389/fpls.2017.01341

[…] 2011). bootstrap values were estimated (with 1000 replicates) to assess the relative support for each branch, and bootstrap values were labeled with cutoff = 50. promoter prediction was operated by plantpan22. sequence data from this article can be found in supplementary table s2., the expression levels of hplcyb, hplcye, hppsy, and hpchyb in algal cells under environmental stresses […]

2017
PMCID: 5725924
PMID: 29228897
DOI: 10.1186/s12870-017-1200-6

[…] to the puc2.1 vector, and several clones were sequenced. dna motifs that bind to myb and bhlh transcription factors were deduced by searching place (http://www.dna.affrc.go.jp/place/) [19] and plantpan (http://plantpan2.itps.ncku.edu.tw/) [20]., amino acid sequences of dfr in other plants and the deduced amino acid sequences of the buckwheat dfrs were aligned using version 2.1 of clustalw […]

2017
PMCID: 5725924
PMID: 29228897
DOI: 10.1186/s12870-017-1200-6

[…] vector, and several clones were sequenced. dna motifs that bind to myb and bhlh transcription factors were deduced by searching place (http://www.dna.affrc.go.jp/place/) [19] and plantpan (http://plantpan2.itps.ncku.edu.tw/) [20]., amino acid sequences of dfr in other plants and the deduced amino acid sequences of the buckwheat dfrs were aligned using version 2.1 of clustalw […]

2016
PMCID: 4905986
PMID: 27379111
DOI: 10.3389/fpls.2016.00788

[…] the cbmv for helpful discussions, especially uri aceituno, francisca aguayo, milagros bracamonte, aliosha figueroa, vicente oliva, and sara zapata., www.rosaceae.org. , blast.ncbi.nlm.nih.gov. , plantpan2.itps.ncku.edu.tw. , http://biotools.umassmed.edu/bioapps/primer3_www.cgi , the supplementary material for this article can be found online at: […]

PlantPAN institution(s)
Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsin-Chu, Taiwan
PlantPAN funding source(s)
Ministry of Science and Technology [MOST 103-2311-B-006–001, MOST 104-2627-M-009–008, MOST 103-2628-B-009-001-MY3, MOST 104-2319-B-400-002 and MOST 103-2911-I-009-101]; Academia Sinica [Innovative Translational Agricultural Research Grant] of the Republic of China

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