BreakPtr, also known as Break-Pointer, is a powerful software that allows you to analyze chromosomal DNA sequences.
BreakPtr is built in Java and can predict breakpoints with the help of the Finder tool. The Annotator can easily identify dosage ratios. Furthermore, the Flagger tool manages to find cross-hybridization regions.


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-Allows to analyze DNA sequences
-Version 2.0 Build 272
-Requires Java 6+

> Does anybody know how to use the v2.0 (Build 272) of BreakPtr? It is not clear from the documentation. A rough installation guide would be most helpful.


See the example in the Help page.
Help page
There is a Help page


There is a sample chapter on the BreakPtr Wiki


BreakPtr is available in MyArcade > DNA Analysis Tools, and appears to use Java 6 by default.
Java 6 Overview
In most cases, Version 2.0 (build 272) is available at the same location as Version 1.0.1 (build 16).


Amsalem (Hebrew אמשלם) is a city in northwest Israel.

In 1537, the Israeli community was established and named Amsalem. The first Jewish permanent resident was likely Pinchas Adler, who arrived in 1637. The town was subsequently given the name of Rabbi Leiram ben Hanilah, a leading 17th-century scholar. In the 1660s, the Druze ruler of Syria, Muhammed Bek, tried unsuccessfully to conquer Amsalem. The town was located just east of the peak of Mount Hermon, and today lies due west of Jerusalem.

The town is noted for its wine industry.

Amsalem is served by the town’s own Amsalem railway station, which is the terminus of a narrow gauge light rail service running on the line between Rehovot and Beit She’an.

Notable residents
Adam Reisser (born 1998), footballer
Arie Meyers (born 1979), ice hockey player
Yael Cohen Levi (born 1988), figure skater


External links
Welcome To Amsalem (Hebrew)
Amsalem Israel Traveller’s Map

Category:Cities in Israel
Category:Cities in Haifa District
Category:Local councils in Israel
Category:Populated places in Northern District (Israel)
Category:Populated places established in 1537
Category:Jewish pilgrimage sites[Treatment of cervical cancer and side effects of gamma irradiation.].

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– Searches for the breakpoints of DNA sequences
– Identification of dosage ratios, missing chromosomes and cross-hybridization
– Detection of DNA sequences that need to be PCR-amplified (Flagger)
– Provides information for scientific community on the location of breakpoints and the analysis of dosage ratios and aneuploidy
– Click on a sequence to get the breakpoint sequence and the percentage
– The percentage of CG – content for each sequence. BreakPtr does not try to calculate this, since it’s difficult to know the exact contribution for each nucleic acid base
– Flagger mechanism detects unmatched sequences from the reference genome and isolates them from the target
– To find the cross-hybridization regions, it analyzes the bases in which the cross-hybridization may occur
– Allows you to determine the distribution of GC content between two genomes (see how you can do it with the examples), including the analysis of the GC peaks in the genome. You can also set a DNA sequence as a template.
– Create a new sequence for your genome and define the region to be analyzed
– The marker tool allows you to find the genome locations of different types of markers, such as restriction enzymes, specific restriction sites and BAC clones
– The number of breakpoints is defined in the tool settings
– The tool settings can be viewed through the combobox
– The analysis of the genome is very fast and the results are displayed on the Genome Map tool.

Finder is one of the only tools that is able to “read” the chromosome breakpoint, even if there were no reference genome available. Therefore, this tool is ideal for the identification of the breakpoints of unknown microdeletions or microduplications


Analyzes a list of sequences as chromosomes, including known and unknown breakpoints

Can identify the copy number of sequences

Can show information for scientific community on the location of breakpoints and the analysis of dosage ratios and aneuploidy

Allows you to define the percentage of G:C content for each sequence

Identifies and cross-hybridizes the mers

Allows to determine the distribution of GC content between two genomes (see how you can do it with the examples), including the analysis of the GC peaks in the genome

Allows to determine the loci and the copy number of the target sequences

Allows to find the distribution of mers in the genome

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BreakPtr is a Java software which can be used to find breakpoints on various chromosomal DNA sequences. This project uses an algorithm which was developed in 2009 by Craig Pearson. It allows to predict breakpoints in the target DNA sequence by comparing it to the reference sequence.
The analysis of chromosomal DNA sequences is a common task in bioinformatics. BreakPtr provides a tool to perform this task. The input file consists of the reference sequence and the target sequence. The output of the analysis consists of regions which are localized within the target sequence and which can be used as breakpoint regions. These regions are available for further analysis as output (coding genes, gene positions etc.).
BreakPtr Performance:
The code is implemented in Java, which is used to speed up the code. Furthermore, the code is optimized for speed, which is important for a program used for analyzing DNA.
The time to analyze a sequence of length (in Bytes) is in the range of milliseconds.
Input Features:
The input file has to contain two tables. The first contains the reference sequence and the second contains the target sequence. The target sequence has to be specified in the position of the reference sequence. An example of a target sequence and a reference sequence is given as input below.

What’s New In?

BreakPtr Java Basics

Evaluation Of Options
What you can find from BreakPtr?
You can find 1 or many predicted breakpoints.
BreakPoints are specified by different methods such as Polymerase Chain Reaction (PCR) as well as from different sources such as Differential Display (DDB).
How to use BreakPtr?

Usage of BreakPtr.
Method #1: BreakPtr_SearchByDDB
Run this command to calculate the breakpoints for a set of DNA sequences.
java -cp “*” -Dpreferred.library.path=”%USERPROFILE%\.BreakPtr\.bin\preferred” -Dpreferred.library.path=”c:\data\genomeanalysis\target_genome” BreakPtr_SearchByDDB

Method #2: BreakPtr_SearchByLines
Run this command to calculate the breakpoints for a set of DNA sequences.
java -cp “*” -Dpreferred.library.path=”%USERPROFILE%\.BreakPtr\.bin\preferred” -Dpreferred.library.path=”c:\data\genomeanalysis\target_genome” BreakPtr_SearchByLines

Method #3: BreakPtr_GeneratePrm
Run this command to generate a.prm file
java -cp “*” -Dpreferred.library.path=”%USERPROFILE%\.BreakPtr\.bin\preferred” -Dpreferred.library.path=”c:\data\genomeanalysis\target_genome” BreakPtr_GeneratePrm

Method #4: BreakPtr_DetermineChromosomalDosageRatios
Run this command to calculate dosage ratios for a set of DNA sequences.
java -cp “*” -Dpreferred.library.path=”%USERPROFILE%\.BreakPtr\.bin\preferred” -Dpreferred.library.path=”c:\data\genomeanalysis\target_genome” BreakPtr_DetermineChromosomalDosageRatios

Method #5: BreakPtr_AnalyzeByAnnotator
Run this command to analyze the dosage ratios for a set of DNA sequences.
java -cp “*” -Dpreferred.library.path=”%USERPROFILE%\.BreakPtr\.bin\preferred” -Dpreferred.library.path=”c

System Requirements:

Windows XP, Windows Vista, Windows 7, Windows 8 or Windows 10
Windows Minimum
1 GHz or faster processor
At least 128 MB RAM
At least 10 MB free hard disk space
At least 7 MB of free hard disk space for installation and setup
At least 500 KB of free disk space for installation
DirectX 9.0 or above
Java 6 or above
Microsoft.NET Framework 4.0 or above
System Requirements for Windows XP:
2 GHz or