The Baksan Neutrino Observatory setups are currently performing search for neutrino and ultra-high-energy gamma ray counterparts of gamma-ray bursts and neutrinos on the GCN/TAN. GCN/TAN (The Gamma-ray Coordinates Network, Transient Astronomy Network) is a system for distributing alerts from gamma-ray bursts, transients. Muon neutrinos and antineutrinos with energies above 1 GeV are registered with the Baksan Underground Scintillation Telescope. Ultra-high-energy gamma rays are registered with the «Carpet-2» setup. Registration of events and analysis of alerts occurs in real time. Alerts from Swift BAT, Fermi GBM, LAT, INTEGRAL, IceCube, HAWC are used. This work presents the description of the alert processing program and preliminary results.