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AllerHunter: AllerHunter is a cross-reactive allergen prediction program built on a combination of Support Vector Machine (SVM) and pairwise sequence similarity. Cross-reactivity is based on similarity of proteins to allergens. However, not all proteins with similar sequence or structure to known allergens are cross-reactive allergens. AllerHunter aims to predict allergens and non-allergens with high sensitivity and specificity, without compromising efficiency at classification of proteins with similar sequence to known allergens. More ...

CNV-seq: a method to detect DNA copy number variation using the next-gen eration high-througput sequencing technologies. The method is based on a robust statistical model that describes the complete analysis procedure and allows the computation of essential confidence values for detection of CNV. More ...

MicroTar pic

MicroTar: an animal miRNA target prediction tool based on miRNA-target complementarity and thermodynamic data. The algorithm uses predicted free energies of unbound mRNA and putative mRNA-miRNA heterodimers, implicitly addressing the accessibility of the mRNA 3-prime untranslated region. MicroTar does not rely on evolutionary conservation to discern functional targets, and is able to predict both conserved and non-conserved targets. More ...


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DNPTrapper: DNPTrapper, a shotgun sequence finishing tool, designed to address the key sequence assembly problems caused by repeated regions in a genome. The program detects and visualizes single nucleotide differences between nearly identical repeat copies, and offers the overview and flexibility needed to rapidly resolve complex regions within a working session. The use of a database allows large amounts of data to be stored and handled, and allows viewing of mammalian size genomes. With DNPTrapper, it is possible to separate repeated regions that previously were considered impossible to resolve, and finishing tasks that previously took days or weeks can be resolved within hours or even minutes. The program is available under an Open Source license. More ...

ReDit pic

ReDit: Repeat Discrepancy Tagger. This is a shotgun assmebly finishing aid. Gap closure and editing is the most time consuming task in genome sequencing. Most of the problems are due to repeated sequences together with sequencing errors. Resulting misassemblies are difficult to correct. ReDit is a tool designed to aid in the finishing process. This program is free. More ...

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