CHAP 10: BIOINFORMATICS

Question 1

interdisciplinary science of collecting, analyzing, and interpreeting biodata

Answer 1

BIOINFORMATICS

Question 2

primarily deals with data derived from GENOM SEQUENCE, PROTEIN STRUCTURES, and GENE EXPRESSION

Answer 2

BIOINFORMATICS

Question 3

bridges gab bet BIOLOGY and COMP SCIENCE

Answer 3

BIOINFORMATICS

Question 4

it represents raw or processed info

Answer 4

BIOLOGICAL DATA

Question 5

5 TYPES OF BIOLOGICAL DATA

Answer 5

1. PROTEIN SEQUENCE
2. NUCLEOTIDE SEQUENCE
3. GENOMIC DATA
4. EXPRESSION DATA
5. STRUCTURAL DATA

Question 6

DNA/RNA sequences

Answer 6

NUCLEOTIDE SEWURNES

Question 7

amino acid chains or proteins

Answer 7

PROTEIN SEQUENCES

Question 8

whole genome seq

Answer 8

GENOMIC DATA

Question 9

data from gene expression

Answer 9

EXPRESSION DATA

Question 10

3D structures of biomolecules

Answer 10

STRUCTURAL DATA

Question 11

organized collection of biological data

Answer 11

BIOINFORMATICS DATABASE

Question 12

TYPES OF BIOLOGICAL DATABASE

Answer 12

1. PRIMARY DATABASE
2. SECONDARY DATABASE
3. TERTIARY DATABASE

Question 13

contain raw data like nucleotide seq (GenBank)

Answer 13

PRIMARY DATABASE

Question 14

contain analyzed and interpreted data (Pfam)

Answer 14

SECONDARY DATABASE

Question 15

provide curated data (OMIM)

Answer 15

TERTIARY DATABASE

Question 16

arranges DNA, RNA, or protein seq to identify regions of similarity

Answer 16

SEQUENCE ALIGNMENT

Question 17

essential for gene annotation, etc

Answer 17

ALIGNMENT

Question 18

TYPES OF SEQUENCE ALIGNMENT:

Answer 18

1. PAIRWISE ALIGNMENT
2. MULTIPLE SEQUENCE ALIGNMENT (MSA)

Question 19

comparison bet 2 alignment (BLAST, etc)

Answer 19

PAIRWISE ALIGNMENT

Question 20

aligning more than 2 sequences (MUSCLE)

Answer 20

MULTIPLE SEQUENCE ALIGNMENT

Question 21

used to score alignments

Answer 21

PAM and BLOSUM

Question 22

identify locations of genes in a genome

Answer 22

GENE PREDICTION

Question 23

assigning functions to the genes

Answer 23

ANNOTATIONS

Question 24

can identify OPEN READING FRAMES (ORF)

Answer 24

tools

Question 25

often us GENE ONTOLOGY terms for standardization

Answer 25

ANNOTATION

Question 26

5 appliactions of bioinformatics

Answer 26

1. DRUG DISCOVERY 2. PERSONALIZED MEDICINE 3. COMPARATIVE GENOMICS 4. FUNCTIONAL GENOMICS 5. SYSTEMS BIOLOGY

Question 27

identification of drugs

Answer 27

DRUG DISCOVERY

Question 28

tailoring treatment based on indiv genetic profiles

Answer 28

PERSONALIZED MEDICINE

Question 29

understanding evol relationship

Answer 29

COMPARATIVE GENOMICS

Question 30

investigating gene functions and regulatory networks

Answer 30

FUNCTIONAL GENOMICS

Question 31

modeling complex interactions

Answer 31

SYSTEMS BIOLOGY

Question 32

_____ is used for sequence alignment (pairwise alignment)

Answer 32

BLAST

Question 33

helps in identifying unkown genes, etc

Answer 33

BLAST

Question 34

use to identify HOMOLOGUS GENES

Answer 34

BLAST

Question 35

used for protein structure prediction

Answer 35

AI & ML in Bioinformatics

Question 36

enables high-resolution understanding of cell specific-exp

Answer 36

SINGLE-CELL OMICS

Question 37

facilitates storage and analaysis of large bio datasets

Answer 37

CLOUD COMPUTING

Question 38

tech like OXFORD NANOPORE improve genome assemblies

Answer 38

LONG-READ SEQUENCING

Question 39

combines GENOMICS, PROTEOMICS, and METABOLOMICS

Answer 39

MULTI-OMICS INTEGRATION

Question 40

bioinformatic tools assist in off-target effect

Answer 40

CRISPR ANALYTICS

Question 41

broad range of techs that allow computers and machines to perform tasks

Answer 41

AI

Question 42

3 AREAS OF AI:

Answer 42

1. MACHINE LEARNING (ML) 2. DEEP LEARNING (DL) 3. NATURAL LANGUAGE PROCESSING (NLP

Question 43

system that learn from data w/o explicit programming

Answer 43

MACHINE LEARNING (ML)

Question 44

subfield of ML

Answer 44

DEEP LEARNING (DL)

Question 45

interaction bet COMPUTERS AND HUMAN LANGUAGES

Answer 45

NATURAL LANGUAGE PROCESSING (NLP)

Question 46

with advent of _____ huge volume of genomics and transcriptomic data are generated

Answer 46

NEXT-GENERATION SEQUENCING (NGS)

Question 47

predict gene locations

Answer 47

GENE ANNOTATION

Question 48

DETECT MUTATIONS

Answer 48

VARIANT CALLING

Question 49

IDENTIFY REGULATORY ELEMENTS

Answer 49

PROMOTORS, ENHANCERS

Question 50

deep learning models such as ___ and ___ can predict splicing patterns

Answer 50

CNNs and RNNs

Question 51

in _____, _____ are fundamental to biological functions

Answer 51

PROTEOMICS, PROTEINS

Question 52

AI MODELS OF PROTEOMICS ARE USED FOR:

Answer 52

1. identifying secondary, tertiary, and quaternary strcutures 2. modeling protein-protein interactions 3. predicting protein stability

Question 53

_____ by ___ uses a convolutiojmal neural network to inerpret sequen

Answer 53

DeepVariant by Google

Question 54

- massive leap - solve decades-old problem of protein folding - predicts structure directly from AA sequence

Answer 54

AlphaFold 2

Question 55

achieved protein prediction comperable to experimental results like X-ray crystallography and cryo-EM

Answer 55

AlphaFold2

Question 56

uses DL to predict bioactivity of molecules

Answer 56

AtomNet

Question 57

backbone for analyyzing images

Answer 57

CONVOLUTIONAL NEURAL NETWORKS (CNNS)

Question 58

____ could classify SKIN CANCER TYPES

Answer 58

DL

Question 59

PROTEIN STURCTURE PREDICTION

Answer 59

AlphaFold2 (predicting 3D protein stucture)

Question 60

GENOMIC VARIANT DETECTION

Answer 60

DeepVariant (CNN-based caller)

Question 61

DRUG DISCOVERY

Answer 61

AtomNet (DL to predicit binding affinity for drug design)

Question 62

CANCER DETECTION

Answer 62

CNN HISTOPATHOLOGY (auto cancer diagnosis)

Question 63

SYNTHETIC BIOLOGY

Answer 63

AI-DRIVEN DESIGN TOOLS (optimizing gene circuits)