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Archived Comments for: GelJ – a tool for analyzing DNA fingerprint gel images

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  1. GelComparII features

    Jónathan Heras, University of La Rioja

    16 September 2015

    Some member of the GelComparII team have recently approached us regarding some aspects of such software that were commented in the paper.

    In Page 6 of the paper, we said "GelComparII does not implement gamma correction". Browsing the GelComparII manual (the main source of documentation for this software, and the one that we used to prepare the paper), the term "gamma correction" is never used. However, the members of GelComparII have explained us that gamma correction is the underlying implementation of two features available in GelComparII called "Enhance weak bands" and "Enhance dark bands".

    In Page 7 of the paper, we said "GelJ is the only tool that offers the lane-by-lane threshold functionality to detect bands automatically". According to the explanations given by the GelComparII team (and reviewing the GelComparII manual), GelComparII also implements a close functionality (a global threshold can be individualised based on the maximum intensity value of each lane), but in a completely different way to the one used in GelJ. That was the reason, while writing our paper, for our misunderstanding of such functionality included in GelComparII.

    Finally, in Additional File 4, we indicated that GelComparII does not include filters for enhancing the quality of the image. Again browsing the GelComparII manual, the word filter is only used in the context of filtering the densitometric curves, and not in the context of pre-processing the image (the latter is the one used in the paper). The members of GelComparII have explained us that, even it is not explicitly indicated in the manual, the feature called "spot removal" is a filter.

    Jónathan Heras (author of the paper) and Katleen Vranckx (Applied Maths, BioInformatics Product Specialist)

    Competing interests

    None declared