Fig. 5.

Maximal spanning windows enable isoform-independent analysis. A maximal spanning window over a set of transcripts (or other genomic features) is defined as the largest possible window surrounding a shared landmark (in this example, a start codon; vertical line), over which the N ^th nucleotide from the landmark in each transcript corresponds to the same genomic position. Maximal spanning windows thus enable position-wise analysis over fractions of genes when isoform distributions are unknown. Plastid uses maximal spanning windows for metagene analysis, measuring sub-codon phasing in ribosome profiling, and estimating ribosomal P-site offsets