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SoftGenetics

SoftGenetics Products - Mutation Explorer


Accuracy of the software in the bi-directional analysis mode is over 99%, with sensitivity to greater than 5% of the primary peak.
Analysis courtesy of Dr. Yidong Bai, Assistant Professor, University of Texas Health Centre, San Antonio TX
Accuracy of the software in the bi-directional analysis mode is over 99%, with sensitivity to greater than 5% of the primary peak.

Mutation Explorer™ - A Diagnostic Tool

Mutation Explorer processes up to 48 lanes, 24 bi-directional, of patient DNA sequence traces. Data input can be from either slab gel or capillary sequencers, using either terminator or primer chemistries. The detection parameters in Explorer have been “sealed” to provide analyst to analyst consistency.

We have built Explorer for ease of use, and quick learning. Normal operation involves only two steps: data input, (Genbank, references and patient traces) followed by review of the differences of the patient to reference as indicated in the mutation electropherogram. Most analysts have found, after becoming familiar with the program’s performance, that peak to peak review of the traces is no longer necessary.

The software automatically forms contigs, performs alignments and mutation detection comparing both forward and reverse patient traces to reference or normal traces. Homozygote and Heterozygote mutations are indicated by sharp peaks in our exclusive mutation electropherogram.

Homozygote Variants are detected when the color of the reference drops 100% being replaced in the same spatial position by a second color in the sample or patient.
The software detects heterozygote variants by observing a drop in color of in the sample vs. the surrounding peaks and the reference, with a second wave length growing in approximately the same proportion and in the same spatial position.
Homozygote Detection
Homozygote Variants are detected when the colour of the reference drops 100% being replaced in the same spatial position by a second colour in the sample or patient.
Heterozygote Detection
The software detects heterozygote variants by observing a drop in colour of in the sample vs. the surrounding peaks and the reference, with a second wave length growing in approximately the same proportion and in the same spatial position.

Insertions and deletions are found by comparing the migration time of the sample to that of the reference, eliminating the false and over calls of other text based comparison software; providing an extremely low false positive rate and . In the event that a heterozygote insertion or deletion is detected, the software will de-convolute the multiple patient trace into two clean traces, while continuing with the mutation detection.

Surveyor and Explorer monitor the migration time of the DNA fragments in comparison to the references. If the program detects a change in the migration time, the center line turns from green to red indicating the presence of an insertion or deletion. The software then re-aligns the traces, to calculate the Indel.
Surveyor and Explorer monitor the migration time of the DNA fragments in comparison to the references. If the program detects a change in the migration time, the center line turns from green to red indicating the presence of an insertion or deletion. The software then re-aligns the traces, to calculate the Indel.
Insertion Detection
Deletion Detection
Surveyor and Explorer monitor the migration time of the DNA fragments in comparison to the references. If the program detects a change in the migration time, the centre line turns from green to red indicating the presence of an insertion or deletion. The software then re-aligns the traces, to calculate the Indel.
The position of the Indel is indicated by the heavy red line.

Assembly of a “whole gene” mutational analysis is easily accomplished. To assemble the mutational analysis of an entire gene simply enter the Genbank data, pre-analysed fragments, and the software will assemble, providing the locations of the found variants in bp order, and calculate an allele frequency.

Reporting is extremely user-friendly with several customer customisable reporting formats, or the customer can easily cut and paste areas of interest to any graphics capable program such as Microsoft Word. Reports can be easily exported in text, XML or HTML formats. Click here to see examples of the reporting feature.

 Download the DNA Variant Analysis PDF PDF icon (1.18Mb)

 

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