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GelQuest DNA Fingerprint Analysis Software
Frequentiy Asked Questions (FAQ)

  • DNA Fingerprint Visualization and Analysis
  • Trial licenses and Software Registration
  • Updating SequentiX software
  • Ordering and Purchasing SequentiX products
  • DNA Fingerprint Visualization and Analysis

      How can I scale the DNA fingerprint trace data of all samples?

      With version 2.1.2 the scaling options have been furtherly improved. To open the scale window double-click onto the panel located right of the DNA fingerprint trace samples. This should show the scaling options for that sample. In the scale window find the button "Apply to all samples". You may use this option to apply the scale parameters of the actual sample to all other ones.

      What kind of data can I import into GelQuest?

      GelQuest reads DNA fingerprint data in various formats. Currently GelQuest imports DNA fingerprint data from the following sources:
    • ABI Prism Sequencers: FSA file format.
    • Beckman Sequencers: SCF file format.
    • Licor Sequencers: TIFF file format.
    • Any DNA fingerprints from electrophoresis gels: almost any common image format.
    • If you have a format that is not currently supported by GelQuest please contact us and we surely find a way to adopt GelQuest to import your data.

      What kind of DNA fingerprints can GelQuest analyze?

      The following DNA fingerprints can be analysed using GelQuest:
    • AFLP: amplified fragment length polymorphism
    • tRFLP: terminal restriction fragment length polymorphism
    • RFLP: restriction fragment length polymorphism
    • PFGE: pulse field gel electrophoresis of chromosomes
    • VNTRs: variable number of trandem repeats (microsatellites)
    • Can I make a final decission which peaks should be present in the binary matrix and which one not?

      GelQuest allows to exclude peaks after peak detection. This can be done either manually for individual peaks or in an automatic mode.
    • To manually exclude a certain peak ("disabling a peak") from the 01 matrix (the hyperbin table) just click it with the right mouse button. This peak can be included again ("enabled") with a second right mouse click.
    • Peaks can also be automatically exclude by changing the hyperbin configuration parameters. Here, you may filter for minimum/maximum base size, peak height, peak area, peak width and peak height to width ratio.
    • How many DNA fingerprints can I see on my screen in a single view?

      GelQuest easily shows over 100 samples on the screen. You can either
    • adjust the row height with the mouse or
    • you can scroll.
    • Why are the size standard peaks of different samples not aligned?

      Each gel run is different. Therefore, we do a sizing of the fragments using a size standard. After appropriate sizing you can switch to view the trace files scaled by base sizes. Then all size standard peaks should be aligned between different samples.

      How does GelQuest save the results of DNA fingerprints analysis?

      GelQuest saves the trace data, the parameters and results of peak recognition in XML format. Therefore, you can easily implement own software packages using the analyzed data from GelQuest analyses.

      If I load a FSA file I do not see any DNA fingerprint trace data. What goes wrong?

      Nothing. FSA files can contain raw data only or both raw and processed data. If you load a FSA file containing raw data only and GelQuest is is the mode to show the processed data you will not see the trace data.
      Here is a short instruction how to see the data:
    • Run GelQuest
    • Click menu FILE --> IMPORT TRACE FILES
    • In the file open dialog select the appropriate file and click OK.
    • Click menu VIEW --> RAW DATA
    • Click menu VIEW --> SCALE BY DATA POINTS
    • To adjust the scales use the scale controls in the panel right of the trace data
    • Can you give me a short protocol how to analyse my fingerprint data?

      This is a short protocol how to detect the peaks in DNA fingerprints:

      Select the samples:

    • With right mouse click select the samples to analyse.
    • Turn off all color channels except the size standard channel (see the color channel control in the toolbar top of the window).
    • Click menu DISPLAY CURVE DATA
    • Double click on the scale bar to open the scale window and adjust the scale if necessary
    • Click ANALYZE icon. [The display will automatically change to SCALE BY DATAPOINTS and to DISPLAY RAW DATA].
    • Peak detection & Analysing the samples:

    • Click SET DEFAULT VALUES if necessary. This will carry out a preliminary peak detection.
    • Explore the trace data: Usually too many peaks were detected.
    • Set the FIRST DATA POINT and LAST DATA POINT values to trim the trace data.
    • Change the MIN PEAK HEIGHT to cut off background noise.
      If you double-clik on the trace data you will see a window showing peak details. Move the mouse over the peaks and explorer their parameters to adjust the peak detection parameters.
    • Select the right size standard definiton or define a new size standard template.
    • Choose the color channel containing the size standard.
    • Click 'Match Standard' button.
    • If too many peaks were detected for the size standard channel GelQuest will not analyse the sample because the size standard matching could be very time consuming and, in addition, erroneous. In this case GelQuest will show a warning message. To analyse these samples try to obtain less peaks by modifying the peak detection parameters.
    • *** IMPORTANT ***
      After peak detection, check whether the size standard peaks of all samples are aligned! If not: optimise the peak detection parameters for those samples that are not aligned and reanalyse.

      What kind of analysis does GelQuest perform?

      GelQuest carries out the following main steps:
    • Import of raw or processed fingerprint data (trace files and gel images). Thus, GelQuest can combine fingerprint data from different sources, e.g. the results of a run on a Licor sequencer with those ones of an ABI sequencer or on a slab gel.
    • Processing of the raw data: smoothing, baselining.
    • Peak detection: recognition of the band pattern
    • Size calibration ("sizing") and the defintion of new size standard templates.
    • Visualisation of the trace data in various formats:
      • Trace view, greyscale and color pseudogel
      • Scale by datapoints or by base size
      • View raw or processed data
      • Highlight or hide peak locations
    • Automatic generation of bins and hypberbins (superbins)
    • Automatic creation of a 01 matrix.
    • How can I furtherly process my DNA fingerprints if they were analysed by GelQuest?
      Can I analyse a binary matrix (01-matrix) with GelQuest?

      By downloading GelQuest you will also receive SequentiX ClusterVis, a tool for the analysis of binary matrix data. It directly takes over the data from GelQuest. ClusterVis analyses 01 matrix data using the following methods:
    • Imports 01 matrix data, distance matrix data, taxon sets, trees.
    • Calculation of distance matrix using various different distance measures:
      • Jaccard (Syn. Jaccard similarity coefficient, Tanimoto similarity, complementary to Soergel distance = (b+c)/(b+c+d))
      • Russel & Rao
      • Rogers & Tanimoto (Syn. Rogers-Tanimoto)
      • Kulczynski #1 (Syn. Tanimoto)
      • Kulczynski #2
      • Dice (Syn. Dice, Sørensen-Dice, Nei & Li, Sørenson’s coefficient, Dice similarity coefficient, Burt coefficient, Pirlot index, Czkanowski, Hodgkin-Richards)
      • Pearson Phi coefficient (Syn. Phi coefficient, Pearson Phi coefficient, Pearson)
      • - bc -
      • Baroni-Urbani/Buser (Syn. Baroni-Urbani, Baroni-Urbani/Buser)
      • Braun-Blanquet
      • Michael
      • Sokal and Sneath #1 (Syn. Sokal and Sneath 1., Anderberg, sometimes "anti-Dice")
      • Sokal and Sneath #2 (Syn. SokalSneath 2, un4)
      • Sokal and Sneath #3 (Syn. SokalSneath 3, un5, "Gower2" [e.g. in ‘Stata’ software])
      • Simple Matching (Syn. Simple Matching, Apostol, Sokal & Michener, Kendall, Zubin, Mean Hamming, "Sokal s measure", Mean Manhattan, Manhattan distance, city block metric, taxi-cab, Mean Hamming distance, Binary Squared Euclidian mean distance, Averaged squared distance)
      • Ochiaï #2 (Syn. Ochiaï #2)
      • Yule Sigma (Syn. Yule Sigma)
      • Hamann (Syn. Hamann, Hamann binary similarity coefficient)
      • Lance & Williams distance (Syn. Lance & Williams distance, Bray-Curtis nonmetric coefficient)
      • Mean Euclidian distance
      • Weighted Euclidian Distance
      • U cost
      • R cost
      • T combined cost
      • Dispersion (Syn. Dispersion, binary dispersion coefficient)
      • Mountford
    • Calculation of dendrograms using Neighbor-Joining and UPGMA clustering methods
    • Resampling tests: bootstrapping, delete-halfjackknifing and jackknifing
    • Principal coordinates analysis
    • Visualisation of cladograms as phylogram, unrootet trees (radial layout), cladogram, elliptogramm, curvogram and rectangular cladogram
    • Export of all data (taxon list, binary matrix, distance matrix, trees, etc.).

    Trial licenses and Software Registration

      What are the system requirements to run GelQuest and ClusterVis?

      Both programs need any 32- or 64-bit Windows operating system and about 10 MB free disc space.

      My trial license expired. Can I get a new trial license?

      The trial licenses are running for 90 days and offer the full range of features. If this time period is too short for you, please contact us and we will find a way.

      I requested a trial license but did not receive it by email. What can I do?

      In some cases it may occure that our trial license notification has been sorted out by a local spam filter on your computer. Please check your email program if the notification has been lost. If not please contact us and we will be glad to help you.

      I did not realize the trial license was specific for the computer that I used for the download itself.

      The trial license is not specific for the download computer but to the computer from which it is requested. You may also request several trial licenses for more than one computer. In this case, request the licenses from each individual computer.

    Updating SequentiX software

    Ordering and Purchasing SequentiX products

      Can I get some tentative price for SequentiX software?

      The actual price for our software products can be easily checked. Either download our order form which contains the acutal prices or check the prices using our online ordering system.

    Didn't find the right answer?

      Contact us and we will help immediately.
    SequentiX - Digital DNA Processing
    Dorfstraße 20
    D-18249 Klein Raden
    Germany
    Phone:
    Fax:
    Email:
    WWW:
    +49 (0)38462-22333
    +49 (0)38462-339807
    Contact us
    www.sequentix.de