You've worked arduously at the task, and as of this spring, 23,254,518 bases of nucleotide sequence have been obtained from the S. sanguis genome, read in segments of about 500 nucleotides. By overlapping the individual reads, you'd expect to cover every position in the 2-million-bp chromosome 11 times! Yet, rather than having a complete sequence, there remains about 200 fragments, called contigs, ranging in size from a few kilobases (kb) to almost 100 kb.

The total amount of DNA sequence contained in the contigs is roughly the size of the genome. This suggests that you are tantalizingly close to completing the sequence. The gaps between the contigs must be very small. How can you fill the gaps?

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