Designing Efficient Spaced Seeds for SOLiD Read Mapping

<table>Building an automaton for <svg height="12.4375" id="M140" style="vertical-align:-0.1638pt" version="1.1" viewbox="0 0 8.6750002 12.4375" width="8.6750002" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink">
<g transform="matrix(.017,-0,0,-.017,.062,12.162)"><path d="M480 416q0 -21 -18 -41q-9 -11 -17 -7q-20 9 -42 9q-62 0 -140 -78q23 -69 88 -192q17 -31 27 -42t20 -11q16 0 62 46l17 -20q-64 -92 -119 -92q-35 0 -70 66q-41 73 -84 187q-36 -30 -62 -61q-27 -115 -35 -172q-41 -8 -78 -20l-6 6l140 612q7 28 0.5 34t-37.5 7l-34 1
l5 26q38 4 74 13.5t57 17t25 7.5q12 0 4 -32l-104 -443h2q35 38 97 93q39 35 65.5 56t62 41.5t58.5 20.5q19 0 30.5 -10t11.5 -22z" id="x1D458"></path></g>
</svg> SNPs and <svg height="12.4375" id="M141" style="vertical-align:-0.1638pt" version="1.1" viewbox="0 0 8.8999996 12.4375" width="8.8999996" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink">
<g transform="matrix(.017,-0,0,-.017,.062,12.162)"><path d="M499 88q-41 -46 -83.5 -73t-68.5 -27q-41 0 -19 98l52 225q10 43 8 59.5t-16 16.5q-37 0 -112 -65t-117 -135q-14 -42 -38 -179q-36 -7 -75 -20l-7 8l127 594q8 40 2.5 49t-35.5 9h-35l5 25q36 3 71.5 13t56.5 18t25 8q11 0 3 -38l-88 -417h2q77 102 195 167q44 24 79 24
q61 0 30 -130l-52 -220q-8 -33 4 -33q8 0 31 14.5t43 33.5z" id="x210E"></path></g>
</svg> color mismatches from a repeated 3-state pattern.</table>

Advances in Bioinformatics

Designing Efficient Spaced Seeds for SOLiD Read Mapping

Figure 5