Computational design of fully overlapping coding schemes for protein pairs and triplets.

ABSTRACT: Gene pairs that overlap in their coding regions are rare except in viruses. They may occur transiently in gene creation and are of biotechnological interest. We have examined the possibility to encode an arbitrary pair of protein domains as a dual gene, with the shorter coding sequence completely embedded in the longer one. For 500 × 500 domain pairs (X, Y), we computationally designed homologous pairs (X', Y') coded this way, using an algorithm that provably maximizes the sequence similarity between (X', Y') and (X, Y). Three schemes were considered, with X' and Y' coded on the same or complementary strands. For 16% of the pairs, an overlapping coding exists where the level of homology of X', Y' to the natural proteins represents an E-value of 10^-10 or better. Thus, for an arbi

SUBMITTER: Opuu V 

PROVIDER: S-EPMC5696523 | biostudies-literature | 2017 Nov

REPOSITORIES: biostudies-literature