An Optimal Seed Based Compression Algorithm for DNA Sequences

<div>Graph comparing compression ratios of HUMDYSTROP against varying <svg height="9.49473pt" id="M97" 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 and the threshold for the number of mismatches allowed being <svg height="12.6721pt" id="M98" style="vertical-align:-3.38377pt" version="1.1" viewbox="-0.0498162 -9.28833 24.9053 12.6721" width="24.9053pt" 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="M238 0V26C174 32 166 38 166 104V712C132 700 70 683 18 677V653C81 647 87 645 87 577V104C87 38 78 32 15 26V0H238Z" id="g121-106"></path><glyph.data ascent="989" descent="-360" horiz-adv-x="253" vert-adv-y="253"></glyph.data></g><g transform="matrix(.013,0,0,-0.013,3.289,0)"><path d="M257 449C165 449 37 374 37 209C37 98 119 -12 256 -12C355 -12 473 65 473 226C473 349 381 449 257 449ZM244 416C333 416 380 320 380 204C380 67 329 21 267 21C184 21 130 115 130 241C130 354 184 416 244 416Z" id="g121-109"></path><glyph.data ascent="989" descent="-360" horiz-adv-x="510" vert-adv-y="510"></glyph.data></g><g transform="matrix(.013,0,0,-0.013,9.919,0)"><path d="M463 437C426 431 375 425 327 422C297 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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="M102" 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 3