e SARS-CoV-2 pandemic

311

quence alignment

312

.1 The issues of sequence alignment

314

7.2.1.1 The three evolution events

315

7.2.1.2 The alignment gap

316

7.2.1.3 The alignment strategy

316

7.2.1.4 The alignment statistic

317

.2 The Sellers algorithm

317

7.2.2.1 The forward propagation stage

318

7.2.2.2 The backward propagation stage

325

.3 The Needleman-Wunsch algorithm

326

7.2.3.1 The initialisation stage

327

7.2.3.2 The forward propagation stage

327

7.2.3.3 The backward propagation stage

329

7.2.3.4 The R library for the Needleman-Wunsch

algorithm

331

.4 The Smith-Waterman algorithm

332

7.2.4.1 The alignment metric and moving directions

332

7.2.4.2 The initialisation

333

7.2.4.3 The forward propagation

334

7.2.4.4 The backward propagation stage

336

7.2.4.5 The R library for the Smith-Waterman algorithm

337

ignment-based multiple sequence comparison

338

ignment-free multiple sequence comparison

343

.1 The k-mers approach

345

.2 The alignment-based approach versus the alignment-free

approach for sequence comparison

352

7.4.2.1 The speed comparison

352

7.4.2.2 The accuracy comparison

353

7.4.2.3 The pattern discovery power

354

mer machine

354

hole genome pattern discovery for SARS-CoV-2

356

6.1 Genomics distribution of sequences

357

6.2 Discrimination between countries based on genomics

pattern

359

6.3 Genomics pattern evolving with time

361

ary

363

ised Peptide Pattern Discovery

364

biological question — protease cleavage pattern discovery

365