Accelerating Smith-Waterman Alignment for Protein Database Search Using Frequency Distance Filtration Scheme Based on CPU-GPU Collaborative System

<div>Dependency of calculating an alignment matrix <svg height="12.7178pt" id="M32" style="vertical-align:-3.42947pt" version="1.1" viewbox="-0.0498162 -9.28833 34.3264 12.7178" width="34.3264pt" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink"><g transform="matrix(.013,0,0,-0.013,0,0)"><path d="M828 650H570L564 622C646 614 650 609 634 524L604 366H253L281 524C296 608 308 615 382 622L388 650H132L126 622C211 615 214 609 198 524L121 122C106 42 102 35 23 28L17 0H276L282 28C196 35 191 40 206 122L243 324H597L559 123C544 42 537 35 452 28L446 0H710L716 28C632 35 628 43 643 122L719 524C735 610 741 615 822 622L828 650Z" id="g113-73"></path><glyph.data ascent="3473" descent="-2876" horiz-adv-x="840" vert-adv-y="840"></glyph.data></g><g transform="matrix(.013,0,0,-0.013,10.923,0)"><path d="M300 -147C201 -63 143 98 143 270S200 602 300 686L282 710C136 610 70 450 70 271V270C70 89 136 -72 282 -170L300 -147Z" id="g113-41"></path><glyph.data ascent="3473" descent="-2876" horiz-adv-x="346" vert-adv-y="346"></glyph.data></g><g transform="matrix(.013,0,0,-0.013,15.421,0)"><path d="M244 607C244 633 228 655 200 655C166 655 146 618 146 594C146 564 166 546 191 546C221 546 244 574 244 607ZM222 91L209 114C184 94 148 66 133 66C127 66 124 73 130 96L201 370C213 416 211 448 191 448C162 448 88 407 29 352L42 328C73 354 104 371 114 371C120 371 119 365 115 345L53 92C32 5 45 -12 68 -12C103 -12 186 50 222 91Z" id="g113-106"></path><glyph.data ascent="3473" descent="-2876" horiz-adv-x="273" vert-adv-y="273"></glyph.data></g><g transform="matrix(.013,0,0,-0.013,18.97,0)"><path d="M95 130C70 130 46 113 46 88C46 72 54 64 59 64C93 55 121 33 121 -3C121 -41 93 -68 44 -88L55 -117C117 -98 186 -56 186 22C186 91 131 130 95 130Z" id="g113-45"></path><glyph.data ascent="3473" descent="-2876" horiz-adv-x="228" vert-adv-y="228"></glyph.data></g><g transform="matrix(.013,0,0,-0.013,24.114,0)"><path d="M394 607C394 634 378 655 350 655C315 655 294 620 294 594C294 564 314 546 339 546C372 546 394 574 394 607ZM360 349C373 414 374 448 351 448C321 448 249 404 183 338L197 313C223 336 265 367 276 367C285 367 283 355 275 313C241 129 220 23 189 -102C175 -158 153 -197 124 -197C106 -197 85 -187 70 -177C64 -173 51 -177 44 -183C34 -193 23 -209 23 -228C23 -244 46 -261 67 -261C86 -261 127 -245 181 -197C237 -147 279 -52 303 66L360 349Z" id="g113-107"></path><glyph.data ascent="3473" descent="-2876" horiz-adv-x="423" vert-adv-y="423"></glyph.data></g><g transform="matrix(.013,0,0,-0.013,29.614,0)"><path d="M275 270C275 450 212 609 64 710L45 686C145 604 203 442 203 270S147 -63 45 -147L64 -170C213 -68 275 89 275 270Z" id="g113-42"></path><glyph.data ascent="3473" descent="-2876" horiz-adv-x="346" vert-adv-y="346"></glyph.data></g></svg>.</div>

International Journal of Genomics

fig1

Figure 1

Figure 1: Accelerating Smith-Waterman Alignment for Protein Database Search Using Frequency Distance Filtration Scheme Based on CPU-GPU Collaborative System 

Figure 1 | Accelerating Smith-Waterman Alignment for Protein Database Search Using Frequency Distance Filtration Scheme Based on CPU-GPU Collaborative System 