Python Programming for Biology: Bioinformatics and Beyond

Figure 17.1.  High-throughput mapping of sequence reads to an indexed genome.

Large numbers of short DNA sequence reads, such as those that come from a ChIP-seq

experiment, may be mapped to a complete genome sequence to identify which positions

they represent. Rather than comparing each short read with the whole genome, many high-

throughput methods map the sequences by using a pre-constructed index, to quickly

connect a large set of sub-sequences with their genome locations. The result of the

mapping is a genomic profile, illustrating any hotspots in the chromosome sequences that

have multiple reads.