We describe techniques for comparing spectra extracted from cosmological
simulations and observational data, using the same methodology to link
Lyman-alpha properties derived from the simulations with properties derived
from observational data. The eventual goal is to measure the coherence or
clustering properties of Lyman-alpha absorbers using observations of quasar
pairs and groups. We quantify the systematic underestimate in opacity that is
inherent in the continuum fitting process of observed spectra over a range of
resolution and signal-to-noise ratio. We present an automated process for
detecting and selecting absorption features over the range of resolution and
signal-to-noise of typical observational data on the Lyman-alpha "forest".
Using these techniques, we detect coherence over transverse scales out to 500
h^{-1}_{50} kpc in spectra extracted from a cosmological simulation at z = 2.Comment: 52 pages, includes 14 figures, to appear in ApJ v566 Feb 200