2HybridTools, a handy software to facilitate clone identification and mutation mapping from yeast two-hybrid screening

Yeast Two-Hybrid (Y2H) and reverse Two-Hybrid (RY2H) are powerful protein–protein interaction screening methods that rely on the interaction of bait and prey proteins fused to DNA binding (DB) and activation domains (AD), respectively. Y2H allows identification of protein interaction partners using screening libraries, while RY2H is used to determine residues critical to a given protein–protein interaction by exploiting site-directed mutagenesis. Currently, both these techniques still rely on sequencing of positive clones using conventional Sanger sequencing. For Y2H, a screen can yield several positives; the identification of such clones is further complicated by the fact that sequencing products usually contain vector sequence. For RY2H, obtaining a complete sequence is required to identify the full range of residues involved in protein–protein interactions. However, with Sanger sequencing limited to 500–800 nucleotides, sequencing is usually carried from both ends for clones greater than this length. Analysis of such RY2H data thus requires assembly of sequencing products combined with trimming of vector sequences and of low-quality bases at the beginning and ends of sequencing products. Further, RY2H analysis requires collation of mutations that abrogate a DB/AD interaction. Here, we present 2HybridTools, a Java program with a user-friendly interface that allows addressing all these issues inherent to both Y2H and RY2H. Specifically, for Y2H, 2HybridTools enables automated identification of positive clones, while for RY2H, 2HybridTools provides detailed mutation reports as a basis for further investigation of given protein–protein interactions.