ARTO - Analysis of Replication Timing and Organization

Software implementation for the algorithm used to analyze ToR data in:

Systematic determination of replication structure highlights interconnections between replication, chromatin structure and nuclear localization,

Shlomit Farkash-Amar, Yaara David, Andreas Polten, Hadas Hezroni, Yonina C. Eldar, Eran Meshorer, Zohar Yakhini and Itamar Simon

 

ARTO

In this website you can download a MATLAB implementation of ARTO (Analysis of Replication Timing and Organization). The software takes raw time of replication (ToR) measurement signals as input and outputs for each genomic location an estimate of its ToR and an association to CTR (constant ToR region) or TTR (Temporal Transition Region).  Please see figure below. Please read the description of input and output parameters for most efficient use of the software.

When using this SW please cite Farkash-Amar et al.

real_data_segmentation_example.png

An example of ARTO segmentation result of chromosome 15 in replicate 2 of mouse lymphoblasts (L1210). Raw data in red, segmented data in regions defined as CTRs or TTRs in black, and in gray – undefined regions where only ToR is determined.


Downloadable files:

ARTO - MATLAB implementation

Running Example

Data for the running example

 

Description of input and output parameters

Inputs to the SW are:

·         locs – a row vector containing the genomic locations of the measured probes.

·         signal – a row vector containing the raw ToR measurements data (should be the same length as locs).

·         fork_rate - a two-elements vector of the fork-rate range in [Kb/min].

·         Sphase_length – S-phase length in [hours].

·          num_reps – number of replicates used in one algorithm run. (optional input).

·         W – window length. Default value is 120. (optional input)

·         min_seg_length – minimal number of points voting for a linear line. Note: the algorithm allows less points if their vote is higher. Default value is 10. (optional input).

·         min_seg0_length – minimal number of points voting for a linear line. Default value is 10. (optional input)

·         plot_hist_flag – a flag indicating whether to plot the histograms of segment length (in bp) and of fork-rate per probe. Default value is false. (optional input)

Outputs of the SW are:

·         SegSignal – the ToR of each genomic location, after the segmentation. (same size as locs)

·         BreakPoints – genomic location of breakpoints between segments.

·         CTIndicator – a cell array which indicates if the genomic location is part of a CTR (‘C’), a TTR (‘T-‘ or ‘T+’) or undefined (‘UD’). (same size as locs)

·         ForkRateVec – an array of the inferred fork-rate for each probe. (same size as locs)