An Optimal Seed Based Compression Algorithm for DNA Sequences

<div>Graph comparing compression ratios against varying <svg height="9.49473pt" id="M88" style="vertical-align:-0.2063999pt" version="1.1" viewbox="-0.0498162 -9.28833 6.66314 9.49473" width="6.66314pt" 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="M480 416C480 431 465 448 438 448C388 448 312 383 252 330C217 299 188 273 155 237H153L257 680C262 700 263 712 253 712C240 712 183 684 97 674L92 648L126 647C166 646 172 645 163 606L23 -6L29 -12C51 -5 77 2 107 8C115 62 130 128 142 180C153 193 179 220 204 241C231 170 259 106 288 54C317 0 336 -12 358 -12C381 -12 423 2 477 80L460 100C434 74 408 54 398 54C385 54 374 65 351 107C326 154 282 241 263 299C296 332 351 377 403 377C424 377 436 372 445 368C449 366 456 368 462 375C472 386 480 402 480 416Z" id="g113-108"></path><glyph.data ascent="3473" descent="-2876" horiz-adv-x="503" vert-adv-y="503"></glyph.data></g></svg> values for different sequences; <svg height="6.1673pt" id="M89" style="vertical-align:-0.2063904pt" version="1.1" viewbox="-0.0498162 -5.96091 7.39387 6.1673" width="7.39387pt" 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="M536 404C536 423 520 448 491 448C445 448 398 404 308 283L286 338C255 416 242 448 217 448C182 448 138 402 92 341L111 321C149 368 169 378 178 378C188 378 198 363 214 320L254 212C185 117 138 65 107 65C98 65 85 69 82 75C79 82 73 86 65 86C44 86 23 60 23 39C23 7 44 -12 71 -12C119 -12 168 33 265 177L306 61C321 17 347 -12 373 -12C413 -12 465 33 507 96L491 119C459 84 432 60 413 60C395 60 378 92 358 148L321 250C341 279 369 310 389 332C417 363 439 382 456 382C466 382 475 376 481 368C486 361 492 358 496 358C513 358 536 381 536 404Z" id="g113-121"></path><glyph.data ascent="3473" descent="-2876" horiz-adv-x="559" vert-adv-y="559"></glyph.data></g></svg>-axis : <svg height="9.51429pt" id="M90" style="vertical-align:-0.2063894pt" version="1.1" viewbox="-0.0498162 -9.3079 17.0891 9.51429" width="17.0891pt" 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="M172 716C109 699 42 656 42 585C42 522 93 485 136 485H137C154 485 180 497 180 523C180 535 172 542 166 543C133 549 104 570 104 606C104 646 133 669 182 689L172 716ZM347 716C284 699 217 656 217 585C217 522 268 485 311 485H312C329 485 355 497 355 523C355 535 348 542 342 543C308 549 279 570 279 606C279 646 308 669 357 689L347 716Z" id="g190-171"></path><glyph.data ascent="989" descent="-360" horiz-adv-x="398" vert-adv-y="398"></glyph.data></g><g transform="matrix(.013,0,0,-0.013,5.193,0)"><path d="M480 416C480 431 465 448 438 448C388 448 312 383 252 330C217 299 188 273 155 237H153L257 680C262 700 263 712 253 712C240 712 183 684 97 674L92 648L126 647C166 646 172 645 163 606L23 -6L29 -12C51 -5 77 2 107 8C115 62 130 128 142 180C153 193 179 220 204 241C231 170 259 106 288 54C317 0 336 -12 358 -12C381 -12 423 2 477 80L460 100C434 74 408 54 398 54C385 54 374 65 351 107C326 154 282 241 263 299C296 332 351 377 403 377C424 377 436 372 445 368C449 366 456 368 462 375C472 386 480 402 480 416Z" id="g113-108"></path><glyph.data ascent="3473" descent="-2876" horiz-adv-x="503" vert-adv-y="503"></glyph.data></g><g transform="matrix(.013,0,0,-0.013,11.733,0)"><path d="M87 710C69 710 43 698 43 671C43 659 50 652 56 651C90 645 119 624 119 588C119 547 90 524 41 504L51 477C114 493 181 537 181 608C181 672 129 710 87 710ZM264 710C247 710 221 698 221 671C221 659 228 652 234 651C267 645 297 624 297 588C297 547 267 524 219 504L228 477C291 493 359 537 359 608C359 672 307 710 264 710Z" id="g190-187"></path><glyph.data ascent="989" descent="-360" horiz-adv-x="401" vert-adv-y="401"></glyph.data></g></svg> value; <svg height="9.39034pt" id="M91" style="vertical-align:-3.42943pt" version="1.1" viewbox="-0.0498162 -5.96091 7.65486 9.39034" width="7.65486pt" 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="M556 393C556 426 537 448 514 448C496 448 478 435 471 420C468 414 462 401 466 394C473 382 480 368 480 346C480 268 392 143 338 67H336C329 163 319 253 309 330S286 448 254 448C215 448 160 383 127 337L143 311C167 344 200 373 208 373S222 365 229 320C246 214 264 66 268 -20C219 -83 131 -171 17 -239L25 -261L137 -235C248 -110 273 -79 335 8C384 77 481 215 520 287C544 332 556 363 556 393Z" id="g113-122"></path><glyph.data ascent="3473" descent="-2876" horiz-adv-x="579" vert-adv-y="579"></glyph.data></g></svg>-axis : compression ratio.</div>

Advances in Bioinformatics

An Optimal Seed Based Compression Algorithm for DNA Sequences

Figure 2