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Figure 6 | BMC Bioinformatics

Figure 6

From: A multiple-alignment based primer design algorithm for genetically highly variable DNA targets

Figure 6

A visual representation of a portion of a 1.4-gigabase, 4.5-million-sequence nucleotide alignment, derived from overlapping 454 reads covering nearly the complete HIV-1 genome, from 35 individual PCR amplicons from a single patient at 5 time-points during infection. The “fin-like” structures reflect the length distributions of reads that begin at each primer site (left-to-right for forward reads, above midline; right-to-left for reverse reads, below midline). In the original image, which has been reduced for printing, each pixel corresponds to a single nucleotide (A, red; C, blue; G, black; T, green). Each vertical grid line represents 5,000 sequence reads; each horizontal grid line, 50 base pairs. The overall number of reads across the genome was fairly constant, indicating similar primer design success and data richness for genetic variability assessments.

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