Figure 1

Overview of V(D)J Partitioning. Partitioning Ig VDJ rearrangements at conserved VH & JH motifs for alignment with the approximate backwards algorithm and other DP algorithms. a) A VDJ nucleotide sequence before subdivision and algorithm processing. The dots between CAG…GTA and GGA…CAG represent the nucleotides that are omitted for brevity. The V and J motifs, TAT TAC TGT and C TGG GG, respectively are shown in bold face type. b) The VDJ rearrangement is divided into 2 sections: the 5’ end of the V-segment containing codons 1–101; and the 3’ end of the V-segment, the VD junction, the D-segment, the DJ junction, and the J-segment. The 5’ end of the V-segment is aligned backwards (3’ to 5’), and the reset of the sequence is aligned forwards (5’ to 3’). The V-end is identified and the two parts of the V are merged. c) The rest of sequence is split just before the J motif, which is where the J-Start DP algorithm aligns the sequence to a J gene (left arrow) and determines the 5’ end of the J-segment. The V-end algorithm is also used to identify the 3’ end of the JH (right arrow). The 5’ and 3’ ends of the J are merged. d) A specialized local DP algorithm is used to align a D-gene within the VD-D-DJ subunit. In the figure, the V-, D-, and J-segments within each partition of the sequence are labeled. The intervening nucleotides labeled VD and DJ represent N addition nucleotides in the junctions.