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ALIDOT specifications


Unique identifier OMICS_23852
Alternative name ALIgned DOT-plots
Software type Application/Script
Interface Command line interface
Restrictions to use Academic or non-commercial use
Input data A sequence alignment and predicted secondary structure predictions for each sequence in the alignment.
Output data A the list of base pairs and a file containing the color-coded dot plot.
Output format TXT
Operating system Unix/Linux
Programming languages Perl
Computer skills Advanced
Version 2.0
Stability Stable
Maintained Yes




No version available


  • person_outline Ivo Hofacker

Additional information

Publications for ALIgned DOT-plots

ALIDOT citations


Wnt Signaling Mediates LTP Dependent Spine Plasticity and AMPAR Localization through Frizzled 7 Receptors

Cell Rep
PMCID: 5946458
PMID: 29694885
DOI: 10.1016/j.celrep.2018.03.119

[…] All data are represented as mean in aligned dot plots unless otherwise stated. Data were obtained from 3 independent experiments unless otherwise stated in the figure legends. We assessed our data for normality using Shapiro-Wilk or Kol […]


Fingolimod therapy is not effective in a mouse model of spontaneous autoimmune peripheral polyneuropathy

Sci Rep
PMCID: 5884804
PMID: 29618748
DOI: 10.1038/s41598-018-23949-4
call_split See protocol

[…] The manuscript was prepared in accordance with ARRIVE guidelines. Data is presented as mean ± sem in aligned dot plots. Clinical scores are shown as median. Data processing and analysis were completed before unblinding of the analyzer. Gaussian distribution of data was checked prior to statistical an […]


DotAligner: identification and clustering of RNA structure motifs

Genome Biol
PMCID: 5747123
PMID: 29284541
DOI: 10.1186/s13059-017-1371-3

[…] of two steps, each considering base pair probabilities: (1) generating a partition function of pairwise probabilistic string alignments and (2) stochastic sampling of string alignments and scoring of aligned dot plots. Existing building blocks are integrated to DotAligner in a novel way. A StrAL-like score is applied during the dynamic programming in step 1, then a CARNA-like score is used to scor […]


Knockdown of amyloid precursor protein increases calcium levels in the endoplasmic reticulum

Sci Rep
PMCID: 5673940
PMID: 29109429
DOI: 10.1038/s41598-017-15166-2

[…] re analysed using Excel or GraphPad Prism software using two-tailed unpaired or one-sample t-tests. The co-localisation data (n = 3–6) with calculated mean values and standard errors are presented in aligned dot plots. One n for the co-localisation analyses is defined as the mean result of six image pairs collected from an independent experiment. The calculated mean values of the Ca2+ measurements […]


A novel sweet potato potyvirus open reading frame (ORF) is expressed via polymerase slippage and suppresses RNA silencing

Mol Plant Pathol
PMCID: 4979677
PMID: 26757490
DOI: 10.1111/mpp.12366

[…] expressed via translational frameshifting, although, in principle, both are compatible with −1 ribosomal frameshifting (reviewed in Firth and Brierley, ). Further, using RNA‐folding software, such as alidot (Hofacker et al., ) and pknotsRG (Reeder et al., ), we failed to predict a convincing 3′ RNA secondary structure at a canonical spacing (i.e. 5–9 nucleotides) downstream of the slippery sites f […]


Characterization and Expression of the Lucina pectinata Oxygen and Sulfide Binding Hemoglobin Genes

PLoS One
PMCID: 4732748
PMID: 26824233
DOI: 10.1371/journal.pone.0147977

[…] ed by dividing it against the average amount of mRNA of the endogenous control in each tissue: mRNA expression = (R0 Target gene)/ (R0 Endogenous control).The mRNA expression levels were presented as aligned dot plots using a logarithmic scale showing means as horizontal bars and standard error of the mean (SEM) with whiskers. The un-paired t test with Welch’s correction, used for samples with une […]


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