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phiSITE specifications

Information


Unique identifier OMICS_03081
Name phiSITE
Restrictions to use None
Maintained Yes

Publication for phiSITE

phiSITE citations

 (6)
call_split

Genomic analysis of WCP30 Phage of Weissella cibaria for Dairy Fermented Foods

2017
PMCID: 5932951
PMID: 29725210
DOI: 10.5851/kosfa.2017.37.6.884
call_split See protocol

[…] ric points of the predicted proteins were calculated with the Compute pI/Mw program (http://www.expasy.ch/tools/pi_tool.html). The promoters and tRNAs were identified with promoter hunter (http://www.phisite.org) and tRNAscan-SE (http://lowelab.ucsc.edu/tRNAscan-SE/), respectively. […]

library_books

Comparative Analysis of Ralstonia solanacearum Methylomes

2017
Front Plant Sci
PMCID: 5390034
PMID: 28450872
DOI: 10.3389/fpls.2017.00504

[…] Upstream regions of interest were analyzed for the presence of promoter elements using three different prediction tools: the Phi-Site Promoter Hunter (phiSITE, RRID:SCR_014754) (Klucar et al., ), PePPER (PePPER Prokaryote Promoter Prediction, RRID:SCR_014740) (de Jong et al., ) and BPROM (SoftBerry, RRID:SCR_000902). Only the strongest prediction of […]

library_books

When Genome Based Approach Meets the “Old but Good”: Revealing Genes Involved in the Antibacterial Activity of Pseudomonas sp. P482 against Soft Rot Pathogens

2016
Front Microbiol
PMCID: 4880745
PMID: 27303376
DOI: 10.3389/fmicb.2016.00782

[…] (Solovyev and Salamov, ). As the PromoterHunter requires a weight matrix for the −10 and −35 sequences, such a matrix was created based on the P. aeruginosa promoters (Potvin et al., ), available at phiSITE. The ARNold program was employed for the identification of rho-independent terminators (Lambert et al., ). […]

call_split

Direct sequencing of human gut virome fractions obtained by flow cytometry

2015
Front Microbiol
PMCID: 4568480
PMID: 26441889
DOI: 10.3389/fmicb.2015.00955
call_split See protocol

[…] ing the ape package (). The frequency of all genera, as well as the ten most frequent genera across the two datasets were compared by Pearson correlations. These sequences were also compared with the phiSITE database containing only viral genomes ().The workflow of the data analysis is shown in Figure . […]

call_split

Genome Analysis of Phage SMSAP5 as Candidate of Biocontrol for Staphylococcus aureus

2015
PMCID: 4682501
PMID: 26761804
DOI: 10.5851/kosfa.2015.35.1.86
call_split See protocol

[…] molecular weight and isoelectric point were calculated with the Compute pI/Mw program (http://www.expasy.ch/tools/pi_tool.html). The promoter and tRNA were identified with promoter hunter (http://www.phisite.org) and tRNAscan- SE program (http://lowelab.ucsc.edu/tRNAscan-SE/), respectively. […]

library_books

Comparing binding site information to binding affinity reveals that Crp/DNA complexes have several distinct binding conformers

2011
Nucleic Acids Res
PMCID: 3159480
PMID: 21586590
DOI: 10.1093/nar/gkr369

[…] ding frame) background pi option to scan using a tab formatted matrix. Pseudo-counts = 1 distributed proportionally to residue priors and pseudo-frequency = 0.01. The program PSSM-convert (http://www.phisite.org/pssm-convert/pssm-convert.htm) was run to check proper matrix tab formatting by converting a count matrix to a sequence logo equal to the Weblogo v2.8.2 (http://weblogo.berkeley.edu/logo.c […]

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phiSITE institution(s)
Institute of Molecular Biology, Slovak Academy of Sciences, Bratislava, Slovakia

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