Two Efficient Techniques to Find Approximate Overlaps between Sequences

<table class="table-group" id="tab4"><tr><td><table class="table"><tr><td class="thead-hr" colspan="10"><hr/></td></tr><tr class="thead"><td class="align_left" rowspan="2">Data Set </td><td class="align_center"><span style="width: 31.5818ptpx;"><svg height="8.55521pt" id="M355" style="vertical-align:-0.2063904pt" version="1.1" viewbox="-0.0498162 -8.34882 31.5818 8.55521" width="31.5818pt" 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="M766 88L752 113C719 83 690 64 681 64C674 64 672 74 679 103L724 292C758 436 724 448 701 448C680 448 666 442 639 429C594 407 514 350 441 252H439L447 289C476 423 450 448 419 448C398 448 379 441 355 427C307 400 234 344 162 249H160L180 324C203 409 197 448 170 448C144 448 82 413 23 349L35 321C57 343 96 374 108 374C115 374 117 371 111 341C87 227 57 112 24 -6L32 -12C53 -4 81 4 108 6C119 68 134 128 149 171C177 229 309 383 364 383C387 383 388 355 373 282C354 190 330 92 303 -6L309 -12C332 -4 356 3 386 6C396 63 411 122 424 171C458 236 590 383 642 383C658 383 664 369 652 315L603 91C587 20 593 -12 619 -12C642 -12 708 23 766 88Z" id="g113-110"></path><glyph.data ascent="3473" descent="-2876" horiz-adv-x="789" vert-adv-y="789"></glyph.data></g><g transform="matrix(.013,0,0,-0.013,13.889,0)"><path d="M535 323V373H52V323H535ZM535 138V188H52V138H535Z" id="g117-34"></path><glyph.data ascent="3473" descent="-2876" horiz-adv-x="587" vert-adv-y="587"></glyph.data></g><g transform="matrix(.013,0,0,-0.013,25.152,0)"><path d="M384 0V27C293 34 287 42 287 114V635C232 613 172 594 109 583V559L157 557C201 555 205 550 205 499V114C205 42 199 34 109 27V0H384Z" id="g113-50"></path><glyph.data ascent="3473" descent="-2876" horiz-adv-x="480" vert-adv-y="480"></glyph.data></g></svg></span></td><td class="align_center"><span style="width: 31.5818ptpx;"><svg height="8.55521pt" id="M356" style="vertical-align:-0.2063904pt" version="1.1" viewbox="-0.0498162 -8.34882 31.5818 8.55521" 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id="g117-34"></path><glyph.data ascent="3473" descent="-2876" horiz-adv-x="587" vert-adv-y="587"></glyph.data></g><g transform="matrix(.013,0,0,-0.013,25.152,0)"><path d="M412 140C382 77 369 73 315 73H129L270 222C362 320 402 379 402 466C402 571 322 635 234 635C177 635 130 609 99 576L42 495L64 475C90 514 133 568 201 568C274 568 318 519 318 435C318 349 255 267 193 193C144 135 87 78 32 23V0H405C417 45 427 89 440 131L412 140Z" id="g113-51"></path><glyph.data ascent="3473" descent="-2876" horiz-adv-x="480" vert-adv-y="480"></glyph.data></g></svg></span></td><td class="align_center"><span style="width: 31.5818ptpx;"><svg height="8.55521pt" id="M357" style="vertical-align:-0.2063904pt" version="1.1" viewbox="-0.0498162 -8.34882 31.5818 8.55521" width="31.5818pt" 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="M766 88L752 113C719 83 690 64 681 64C674 64 672 74 679 103L724 292C758 436 724 448 701 448C680 448 666 442 639 429C594 407 514 350 441 252H439L447 289C476 423 450 448 419 448C398 448 379 441 355 427C307 400 234 344 162 249H160L180 324C203 409 197 448 170 448C144 448 82 413 23 349L35 321C57 343 96 374 108 374C115 374 117 371 111 341C87 227 57 112 24 -6L32 -12C53 -4 81 4 108 6C119 68 134 128 149 171C177 229 309 383 364 383C387 383 388 355 373 282C354 190 330 92 303 -6L309 -12C332 -4 356 3 386 6C396 63 411 122 424 171C458 236 590 383 642 383C658 383 664 369 652 315L603 91C587 20 593 -12 619 -12C642 -12 708 23 766 88Z" id="g113-110"></path><glyph.data ascent="3473" descent="-2876" horiz-adv-x="789" vert-adv-y="789"></glyph.data></g><g transform="matrix(.013,0,0,-0.013,13.889,0)"><path d="M535 323V373H52V323H535ZM535 138V188H52V138H535Z" id="g117-34"></path><glyph.data ascent="3473" descent="-2876" horiz-adv-x="587" vert-adv-y="587"></glyph.data></g><g transform="matrix(.013,0,0,-0.013,25.152,0)"><path d="M285 378C315 398 338 416 353 432C373 451 384 474 384 503C384 579 325 635 236 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441 355 427C307 400 234 344 162 249H160L180 324C203 409 197 448 170 448C144 448 82 413 23 349L35 321C57 343 96 374 108 374C115 374 117 371 111 341C87 227 57 112 24 -6L32 -12C53 -4 81 4 108 6C119 68 134 128 149 171C177 229 309 383 364 383C387 383 388 355 373 282C354 190 330 92 303 -6L309 -12C332 -4 356 3 386 6C396 63 411 122 424 171C458 236 590 383 642 383C658 383 664 369 652 315L603 91C587 20 593 -12 619 -12C642 -12 708 23 766 88Z" id="g113-110"></path><glyph.data ascent="3473" descent="-2876" horiz-adv-x="789" vert-adv-y="789"></glyph.data></g><g transform="matrix(.013,0,0,-0.013,13.889,0)"><path d="M535 323V373H52V323H535ZM535 138V188H52V138H535Z" id="g117-34"></path><glyph.data ascent="3473" descent="-2876" horiz-adv-x="587" vert-adv-y="587"></glyph.data></g><g transform="matrix(.013,0,0,-0.013,25.152,0)"><path d="M384 0V27C293 34 287 42 287 114V635C232 613 172 594 109 583V559L157 557C201 555 205 550 205 499V114C205 42 199 34 109 27V0H384Z" id="g113-50"></path><glyph.data ascent="3473" descent="-2876" horiz-adv-x="480" vert-adv-y="480"></glyph.data></g></svg></span></td><td class="align_center"><span style="width: 31.5818ptpx;"><svg height="8.55521pt" id="M359" style="vertical-align:-0.2063904pt" version="1.1" viewbox="-0.0498162 -8.34882 31.5818 8.55521" width="31.5818pt" 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="M766 88L752 113C719 83 690 64 681 64C674 64 672 74 679 103L724 292C758 436 724 448 701 448C680 448 666 442 639 429C594 407 514 350 441 252H439L447 289C476 423 450 448 419 448C398 448 379 441 355 427C307 400 234 344 162 249H160L180 324C203 409 197 448 170 448C144 448 82 413 23 349L35 321C57 343 96 374 108 374C115 374 117 371 111 341C87 227 57 112 24 -6L32 -12C53 -4 81 4 108 6C119 68 134 128 149 171C177 229 309 383 364 383C387 383 388 355 373 282C354 190 330 92 303 -6L309 -12C332 -4 356 3 386 6C396 63 411 122 424 171C458 236 590 383 642 383C658 383 664 369 652 315L603 91C587 20 593 -12 619 -12C642 -12 708 23 766 88Z" id="g113-110"></path><glyph.data ascent="3473" descent="-2876" horiz-adv-x="789" vert-adv-y="789"></glyph.data></g><g transform="matrix(.013,0,0,-0.013,13.889,0)"><path d="M535 323V373H52V323H535ZM535 138V188H52V138H535Z" id="g117-34"></path><glyph.data ascent="3473" descent="-2876" horiz-adv-x="587" vert-adv-y="587"></glyph.data></g><g transform="matrix(.013,0,0,-0.013,25.152,0)"><path d="M412 140C382 77 369 73 315 73H129L270 222C362 320 402 379 402 466C402 571 322 635 234 635C177 635 130 609 99 576L42 495L64 475C90 514 133 568 201 568C274 568 318 519 318 435C318 349 255 267 193 193C144 135 87 78 32 23V0H405C417 45 427 89 440 131L412 140Z" id="g113-51"></path><glyph.data ascent="3473" descent="-2876" horiz-adv-x="480" vert-adv-y="480"></glyph.data></g></svg></span></td><td class="align_center"><span style="width: 31.5818ptpx;"><svg height="8.55521pt" id="M360" style="vertical-align:-0.2063904pt" version="1.1" 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324C203 409 197 448 170 448C144 448 82 413 23 349L35 321C57 343 96 374 108 374C115 374 117 371 111 341C87 227 57 112 24 -6L32 -12C53 -4 81 4 108 6C119 68 134 128 149 171C177 229 309 383 364 383C387 383 388 355 373 282C354 190 330 92 303 -6L309 -12C332 -4 356 3 386 6C396 63 411 122 424 171C458 236 590 383 642 383C658 383 664 369 652 315L603 91C587 20 593 -12 619 -12C642 -12 708 23 766 88Z" id="g113-110"></path><glyph.data ascent="3473" descent="-2876" horiz-adv-x="789" vert-adv-y="789"></glyph.data></g><g transform="matrix(.013,0,0,-0.013,13.889,0)"><path d="M535 323V373H52V323H535ZM535 138V188H52V138H535Z" id="g117-34"></path><glyph.data ascent="3473" descent="-2876" horiz-adv-x="587" vert-adv-y="587"></glyph.data></g><g transform="matrix(.013,0,0,-0.013,25.152,0)"><path d="M412 140C382 77 369 73 315 73H129L270 222C362 320 402 379 402 466C402 571 322 635 234 635C177 635 130 609 99 576L42 495L64 475C90 514 133 568 201 568C274 568 318 519 318 435C318 349 255 267 193 193C144 135 87 78 32 23V0H405C417 45 427 89 440 131L412 140Z" id="g113-51"></path><glyph.data ascent="3473" descent="-2876" horiz-adv-x="480" vert-adv-y="480"></glyph.data></g></svg></span></td><td class="align_center"><span style="width: 31.5818ptpx;"><svg height="8.55521pt" id="M363" style="vertical-align:-0.2063904pt" version="1.1" viewbox="-0.0498162 -8.34882 31.5818 8.55521" width="31.5818pt" 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="M766 88L752 113C719 83 690 64 681 64C674 64 672 74 679 103L724 292C758 436 724 448 701 448C680 448 666 442 639 429C594 407 514 350 441 252H439L447 289C476 423 450 448 419 448C398 448 379 441 355 427C307 400 234 344 162 249H160L180 324C203 409 197 448 170 448C144 448 82 413 23 349L35 321C57 343 96 374 108 374C115 374 117 371 111 341C87 227 57 112 24 -6L32 -12C53 -4 81 4 108 6C119 68 134 128 149 171C177 229 309 383 364 383C387 383 388 355 373 282C354 190 330 92 303 -6L309 -12C332 -4 356 3 386 6C396 63 411 122 424 171C458 236 590 383 642 383C658 383 664 369 652 315L603 91C587 20 593 -12 619 -12C642 -12 708 23 766 88Z" id="g113-110"></path><glyph.data ascent="3473" descent="-2876" horiz-adv-x="789" vert-adv-y="789"></glyph.data></g><g transform="matrix(.013,0,0,-0.013,13.889,0)"><path d="M535 323V373H52V323H535ZM535 138V188H52V138H535Z" id="g117-34"></path><glyph.data ascent="3473" descent="-2876" horiz-adv-x="587" vert-adv-y="587"></glyph.data></g><g transform="matrix(.013,0,0,-0.013,25.152,0)"><path d="M285 378C315 398 338 416 353 432C373 451 384 474 384 503C384 579 325 635 236 635H235C182 635 136 610 108 579L65 516L85 496C110 533 150 575 205 575C258 575 300 543 300 481C300 407 232 369 141 339L147 310C163 315 188 321 211 321C268 321 338 284 338 192C338 94 288 40 217 40C160 40 119 68 93 91C85 98 77 97 69 91C60 84 47 71 46 58C44 46 48 35 62 22C75 10 116 -12 162 -12C234 -12 424 62 424 224C424 297 373 359 285 376V378Z" id="g113-52"></path><glyph.data ascent="3473" descent="-2876" horiz-adv-x="480" vert-adv-y="480"></glyph.data></g></svg></span></td></tr><tr class="thead"><td class="align_center"> PT </td><td class="align_center"> PT </td><td class="align_center"> PT </td><td class="align_center"> PH </td><td class="align_center"> PH </td><td class="align_center"> PH </td><td class="align_center"> FM </td><td class="align_center"> FM </td><td class="align_center"> FM </td></tr><tr><td class="thead-hr" colspan="10"><hr/></td></tr><tr><td class="align_left"><i>Citrus clementina </i></td><td class="align_center">122</td><td class="align_center"> 1094</td><td class="align_center"> 5749</td><td class="align_center"> 16</td><td class="align_center">42</td><td class="align_center">392</td><td class="align_center"> 54</td><td class="align_center"> 200</td><td class="align_center"> 1377</td></tr><tr><td class="align_left"><i>Citrus sinensis </i></td><td class="align_center"> 233</td><td class="align_center"> 2229</td><td class="align_center"> 12053</td><td class="align_center"> 49</td><td class="align_center">361</td><td class="align_center">1352</td><td class="align_center"> 100</td><td class="align_center"> 442</td><td class="align_center"> 3501</td></tr><tr><td class="align_left"><i>Citrus trifoliata </i></td><td class="align_center"> 30</td><td class="align_center"> 223</td><td class="align_center"> 1069</td><td class="align_center"> 10.5</td><td class="align_center">45</td><td class="align_center">158</td><td class="align_center"> 24</td><td class="align_center"> 92</td><td class="align_center"> 660</td></tr><tr><td class="align_left"><i>C. elegans </i></td><td class="align_center"> 381</td><td class="align_center"> 3681</td><td class="align_center"> 21390</td><td class="align_center"> 104</td><td class="align_center">241</td><td class="align_center">1682</td><td class="align_center"> 186</td><td class="align_center"> 792</td><td class="align_center"> 4806</td></tr><tr><td class="align_left">SRR2244250</td><td class="align_center"> 757</td><td class="align_center"> 8111</td><td class="align_center"> 30234</td><td class="align_center"> 49</td><td class="align_center">151</td><td class="align_center">6023</td><td class="align_center"> 357</td><td class="align_center"> 2340</td><td class="align_center"> 16161</td></tr><tr><td class="align_left">SRR500004</td><td class="align_center"> 3502</td><td class="align_center"> 20342</td><td class="align_center"> 90321</td><td class="align_center"> 252</td><td class="align_center">1414</td><td class="align_center">8752</td><td class="align_center"> 1787</td><td class="align_center"> 6813</td><td class="align_center"> 44907</td></tr><tr class="table-tr"><td colspan="10"><hr class="tbody-hr"/></td></tr></table></td></tr></table>

Time consumptions for prefix tree (PT), pigeonhole (PH) and FM solutions to find approximate overlaps when real data is used on a capable AWS node. Time is shown in seconds.

BioMed Research International

tab4

Table 4

Table 4: Two Efficient Techniques to Find Approximate Overlaps between Sequences 