Control Elements Secondary Structures of HIV-1 genome

The CESSHIV-1 database currently contains the secondary structures of control elements located in the 5' and 3' untranslated regions of HIV-1 genomic pre-mRNA and analitycal phylogenetic information on these elements. The primary sequences of the HIV-1 genomic region encompassing control elements and general information about HIV-1 isolates (subtype, country, sampling year and patient) have been extracted from the Entrez Nucleotide database of NCBI (http://www.ncbi.nlm.nih.gov/), HIV sequence database of Los Alamos National Laboratory (http://www.hiv.lanl.gov/) and also scientific periodicals. In addition to accession number each HIV-1 isolate in the CESSHIV-1 database is also assigned with a database number to make statistical data easy-to-use.

Various models for the 5' terminal region of HIV-1 are reported in recent publications. Currently in our database the secondary structures of PBS region and DIS, SD, Psi region are given in the context of the BMH model of Abbink and Berkhout (2003). The local folding of DIS, SD, Psi region is also compatible with a new model of dimer linkage sequence proposed by Sakuragi et al. (Nucleic Acids Research, 2012, Advance Access). The secondary structures have been predicted by mfold program of M. Zuker (2003).

The database staff includes biophysicists, molecular biologists and software programmer. We are a part of the Molecular and Quantum Biophysics Department of the Institute of Molecular Biology and Genetics of National Academy of Ukraine. The database was developed within the project under Research Partnership Program of the Scientific Technological Center of Ukraine and EU.

Questions or comments? Contact us at cesshiv1@gmail.com