|
|||||
|
|
Identification of regions in multiple sequence alignments thermodynamically suitable for targeting by consensus oligonucleotides: application to HIV genome |
|
| Authors: | Olga?V?Matveeva Brian?T?Foley Vladimir?A?Nemtsov Raymond?F?Gesteland Senya?Matsufuji John?F?Atkins Aleksey?Y?Ogurtsov |
| Institution: | (1) Department of Human Genetics, University of Utah, Salt Lake City, 84112-5330, USA;(2) Los Alamos National Laboratory, , P.O. Box 1663, Los Alamos, NM 87545, USA;(3) MGGT, Ul. Lavochkina 23(A), 125502 Moscow, Russia;(4) Department of Biochemistry II, The Jikei University School of Medicine, 3-25-8 Nishi-Shinbashi, Minato-ku Tokyo, 105-8461, Japan;(5) Biosciences Institute, University College Cork, Cork, Ireland;(6) National Center for Biotechnology Information, NLM, NIH, Bethesda, Maryland 20814, USA |
| Abstract: | BackgroundComputer programs for the generation of multiple sequence alignments such as "Clustal W" allow detection of regions that are most conserved among many sequence variants. However, even for regions that are equally conserved, their potential utility as hybridization targets varies. Mismatches in sequence variants are more disruptive in some duplexes than in others. Additionally, the propensity for self-interactions amongst oligonucleotides targeting conserved regions differs and the structure of target regions themselves can also influence hybridization efficiency. There is a need to develop software that will employ thermodynamic selection criteria for finding optimal hybridization targets in related sequences. |
| Keywords: | |
| 本文献已被 SpringerLink 等数据库收录！ | |