Similarity blocks found by applying the N-local decoding method (for N = 11) to the HIV non-coding LTR sequences. This is a nucleotide sequences alignment of the 43 non-coding LTR sequences that are used in the Results section corresponding to Figures 2-4. The alignment is focused on the NFKB binding site (GGGACTTTCCA/G) and its flanking sequences. Most often, the similarity blocks are aligned. In the left columns, the sequences are given by their database accession numbers followed by their nomenclature (HIV-1; HIV-2; SIV-CPZ-CAM 3; -CAM 5; -GAB; -US; SIV-SMM; SIV-SMM-MAC) and their groups, subtypes and sub-subtypes (for HIV-1 and HIV-2). The sequences are re-grouped according to the phylogeny as seen in Figures 1-4. The letters are re-written by applying the N-local decoding method (N = 11). When the identifier contains a number with more than one digit, this number is replaced by a #. Identical recoded letters that are in the same column are written using the same colour. The sequences are written from the left to the right. The coordinate of the first letter in the file hivltr.fsa , is indicated at the left of this first letter of each sequence displayed. When several sequences are re-grouped because they are identical (for instance 6 HIV-2-A sequences), the lowest and the highest coordinates are indicated. The sequences are often written in several lines to show similarities between sequences and parts of sequences.
Didier et al. BMC Bioinformatics 2007 8:1 doi:10.1186/1471-2105-8-1