MoLoTool is an interactive web application to scan DNA sequences for transcription factor binding sites (TFBS) with position weight matrices presented in HOCOMOCO model collection. The sequence markup is text-based and can be easily copied and pasted via clipboard to any MS-Word-type text editor while maintaining colored motif occurrences.

HOmo sapiens COmprehensive MOdel COllection (HOCOMOCO) contains Transcription Factor (TF) binding models for human and mouse TFs represented as classic Position Weight Matrices (PWMs, also known as Position-Specific Scoring Matrices, PSSMs) and precalculated score thresholds (see HOCOMOCO website for details).

The following browsers are supported - Google Chrome v.49+, Firefox v.45+, Opera v.35+. Any technical questions should be addressed to Evgeniy Ruminsky, Ivan Kulakovskiy and Ilya Vorontsov or directly to the Issues page on Github.

A basic example shown with button .

To clear changes and return to the default state use .

The example is taken from Schwartz et al. 2017 and shows EBF1 (COE1) TF binding site present in SLAMF1 human promoter but absent in the respective orthologous mouse promoter. The demo visualization can be reproduced by with the step-by-step guide.

First, add binding models from HOCOMOCO to the models list. To perform this step, start browsing models by typing TF name or family in the search field (). Click on a Motif ID () in the drop-down list and a new motif will appear below.

Note that chosen Motif ID COE1_HUMAN.H11MO.0.A contains a Hyperlink to the HOCOMOCO database.

Click the button or type/paste sequences manually. FASTA format is supported. The allowed alphabet is - {A, a, T, t, G, g, C, c, N, n}.

Note that PWM score = 0 is assigned to {N, n} letters.

Click to parse the sequences. Separated Tabs will be created for each sequence in the list.

Switch the button to “Yes”, if you want to clear all previously parsed sequences on submit.

If there are no parsing errors, multiple (one-per-sequence) new Tabs () will be created in the field below. To see the name of a particular sequence click .

As long as the list of chosen binding modes is not empty, the predicted binding sites will be visually marked in the sequences.

To copy the markup click the Copy icon (). Font size () and Color can be adjusted if necessary.

To compare several sequences at once, switch mode to Multiple with the button. Use Lock (, ) to prevent a particular tab from horizontal scrolling. An important note. In this mode the table with the TFBS predictions at the bottom of the page includes predictions for ALL sequences.

To visualize binding sites for a single sequence switch mode to Single (). An important note. In this mode the table will contain sites only for the ACTIVE, currently visible sequence.

Set desired motif P-value precisely or by dragging the slider. The value is shown in both linear and logarithmic scale and restricted to the [ 1.00e-6, 5.00e-2 ] interval. You may experience a minor slowdown when visualizing TFBS for long sequences (100bp+).

The recommended permissive P-value = 0.0005 (approximately 1 expected prediction in a stretch of random 1000 nucleotides of double-stranded DNA). Check [HOCOMOCO v9] for details.

Detailed data on detected binding sites are provided in the table at the bottom of the page. The population of the complete table is the most time-consuming operation. To maintain overall page responsiveness while tweaking settings the table can be switched off using the button.

The table has additional controls. can be used to show additional data on predicted TFBS. Info button () unfolds additional information directly within the table.

The table contents can be saved using Export buttons (). The results can be filtered with the Search field ().

An important note. According to the chosen Mode ( - Single, - Multiple) the table will contain different sites. They are either from all sequences or from the single active sequence visualized. Details are given above in the Add sequences part of the guide.