Paul A. Gagniuc - Algorithms in Bioinformatics

301 301

302 302

303 303

304 304

305 305

306 306

307 307

308 308

309 309

310 310

311 311

312 312

313 313

314 314

315 315

316 316

317 317

318 318

319 319

320 320

321 321

322 322

323 323

324 324

325 325

326 326

327 327

328 328

329 329

330 330

331 331

332 332

333 333

334 334

335 335

336 336

337 337

338 338

339 339

340 340

341 341

342 342

343 343

344 344

345 345

346 347

347 348

348 349

349 350

350 351

351 352

352 353

353 354

354 355

355 356

356 357

357 358

358 359

359 360

360 361

361 362

362 363

363 364

364 365

365 366

366 367

367 368

368 369

369 370

370 371

371 372

372 373

373 374

374 375

375 376

376 377

377 378

378 379

379 380

380 381

381 382

382 383

383 384

384 385

385 386

386 387

387 388

388 389

389 391

390 392

391 393

392 394

393 395

394 396

395 397

396 398

397 399

398 400

399 401

400 402

401 403

402 404

403 405

404 406

405 407

406 408

407 409

408 410

409 411

410 412

411 413

412 414

413 415

414 416

415 417

416 418

417 419

418 420

419 421

420 422

421 423

422 424

423 425

424 426

425 427

426 428

427 429

428 430

429 431

430 432

431 433

432 434

433 435

434 436

435 437

436 438

437 439

438 441

439 442

440 443

441 444

442 445

443 446

444 447

445 448

446 449

447 450

448 451

449 452

450 453

451 454

452 455

453 456

454 457

455 458

456 459

457 460

458 461

459 462

460 463

461 464

462 465

463 467

464 468

465 469

466 470

467 471

468 472

469 473

470 474

471 475

472 476

473 477

474 478

475 479

476 480

477 481

478 482

479 483

480 484

481 485

482 486

483 487

484 489

485 490

486 491

487 492

488 493

489 494

490 495

491 496

492 497

493 498

494 499

495 500

496 501

497 502

498 503

Paul A. Gagniuc

University Politehnica of Bucharest

Bucharest, Romania

This first edition first published 2021

© 2021 John Wiley & Sons, Inc.

All rights reserved. No part of this publication may be reproduced, stored in a retrieval system, or transmitted, in any form or by any means, electronic, mechanical, photocopying, recording or otherwise, except as permitted by law. Advice on how to obtain permission to reuse material from this title is available at http://www.wiley.com/go/permissions.

The right of Paul A. Gagniuc to be identified as the author of this work has been asserted in accordance with law.

Registered Office

John Wiley & Sons, Inc., 111 River Street, Hoboken, NJ 07030, USA

Editorial Office

111 River Street, Hoboken, NJ 07030, USA

For details of our global editorial offices, customer services, and more information about Wiley products visit us at www.wiley.com.

Wiley also publishes its books in a variety of electronic formats and by print-on-demand. Some content that appears in standard print versions of this book may not be available in other formats.

Limit of Liability/Disclaimer of Warranty

The contents of this work are intended to further general scientific research, understanding, and discussion only and are not intended and should not be relied upon as recommending or promoting scientific method, diagnosis, or treatment by physicians for any particular patient. In view of ongoing research, equipment modifications, changes in governmental regulations, and the constant flow of information relating to the use of medicines, equipment, and devices, the reader is urged to review and evaluate the information provided in the package insert or instructions for each medicine, equipment, or device for, among other things, any changes in the instructions or indication of usage and for added warnings and precautions. While the publisher and authors have used their best efforts in preparing this work, they make no representations or warranties with respect to the accuracy or completeness of the contents of this work and specifically disclaim all warranties, including without limitation any implied warranties of merchantability or fitness for a particular purpose. No warranty may be created or extended by sales representatives, written sales materials or promotional statements for this work. The fact that an organization, website, or product is referred to in this work as a citation and/or potential source of further information does not mean that the publisher and authors endorse the information or services the organization, website, or product may provide or recommendations it may make. This work is sold with the understanding that the publisher is not engaged in rendering professional services. The advice and strategies contained herein may not be suitable for your situation. You should consult with a specialist where appropriate. Further, readers should be aware that websites listed in this work may have changed or disappeared between when this work was written and when it is read. Neither the publisher nor authors shall be liable for any loss of profit or any other commercial damages, including but not limited to special, incidental, consequential, or other damages.

Library of Congress Cataloging-in-Publication Data

Names: Gagniuc, Paul A., author.

Title: Algorithms in bioinformatics : theory and implementation / Paul A. Gagniuc, Polytechnic University of Bucharest, Bucharest, Romania.

Description: First edition. | Hoboken, NJ : Wiley, 2021. | Includes bibliographical references and index.

Identifiers: LCCN 2021004386 (print) | LCCN 2021004387 (ebook) | ISBN 9781119697961 (cloth) | ISBN 9781119697954 (adobe pdf) | ISBN 9781119697992 (epub)

Subjects: LCSH: Bioinformatics. | Algorithms.

Classification: LCC QH324.2 .G34 2021 (print) | LCC QH324.2 (ebook) | DDC 570.285–dc23

LC record available at https://lccn.loc.gov/2021004386

LC ebook record available at https://lccn.loc.gov/2021004387

Cover Design: Wiley

Cover Image: © Science Photo Library/Alamy Stock Photo

I dedicate this book to my family,

my children Nichita and Ana,

my beautiful wife Elvira,

and to my mother-in-law Anastasia.

Algorithms in Bioinformatics: Theory and Implementation is a concise yet comprehensive textbook of bioinformatics, which describes some of the main algorithms that are used to elucidate biological functions and relationships. This unique guide to Algorithms in Bioinformatics approaches the subject along the four convergent lines of mathematics, implementation, simulation, experimentation, and can be ideal for upper-undergraduate bioinformatics courses, researchers, doctoral students, and sociologists or engineers charged with data analysis. This work first begins with a general introduction to biology, which is meant to bring a more concrete understanding of the molecular processes concerning the field of bioinformatics. Following this introduction, an in-detail look is made to subjects like sequence alignment, forced alignment, detection of motifs, sequence logos, Markov chains, or information entropy. Other novel approaches are also described, such as self-sequence alignment, objective digital stains (ODSs) or spectral forecast, and the discrete probability detector (DPD) algorithm. This work also contains thorough step-by-step explanations regarding the meaning of the background models in bioinformatics from several angles. More importantly, it introduces the readers to the art of algorithms, shows how to design computer implementations, and provides extensive worked examples with detailed case studies. The implementations presented here point out how native programming in Javascript can broaden the horizons of possibilities in bioinformatics by considering the might of modern Internet browsers. Graphical illustrations are used for technical details on computational algorithms to aid an in-depth understanding of their inner workings. Moreover, this work brings to the reader's attention more than 100 open-source implementations and 33 Powerpoint presentations.