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Biostatistics > Introduction > Flashcards

Introduction Flashcards

1
Q

What is Bioinformatics?

A

Application of computer sciences to biology

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2
Q

What are the main computational challenges?

A
  • Data acquisition, tracking and preliminary analysis
  • High quantity of storage, computing power and specialized software requirements
  • Model creation
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3
Q

Name some research areas of Bioinformatics

A

Sequence analysis and function prediction
Protein structure analysis and prediction
Comparative genomics, evolutionary biology
Gene and protein expression
PPI
Proteomics

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4
Q

What are the types of tools used in bioinformatics?

A
  • Databases
  • Softwares
  • Servers
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5
Q

Main Service centers

A
  • NCBI
  • EBI
  • CIB
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6
Q

What are the properties of model organisms?

A

-Easy mainteinance & breed
-Selected for specific purposes
Experimental
Genetic
Genomic
-Good for specific purposes

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7
Q

What is a database?

A

A collection of related data that is structured, searchable, updated periodically and cross-referenced. It includes the tools necesary for acces, updating and information management. Each has a specific format for data storage.

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8
Q

Most important databases

A

Table —Page 8

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9
Q

What is a server?

A

Computer from an institure that provides services to other computers (db storage and associated tools)

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10
Q

Main servers?

A 
Expasy
Uniprot
NCBI
EBI
Japanese Genome net
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11
Q

What types of life sciences databases?

A 
Nucleotide sequences (DNA, RNA)
Genomics
Mutation/polymorphism 
Protein sequences
Protein domain/family
Proteomics
3D structure
Metabolism/ pathways
Bibliography
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12
Q

What are the main nucleotide seq. Databases?

A

EMBL/ENA (Europe)
GenBank (USA)
DDBJ (Japan)

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13
Q

What are genomic db?

A

Databases that contain information on gene chromosomal location (mapping), nomenclature and provide links to sequence db. Usually contain no sequences.

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14
Q

Examples of genomic db

A

MIM, GDB (human) , MGD (mouse), Flybase (Drosophila), SGD (yeast), MaizeDB.

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15
Q

Examples of genome browsers

A

Ensembl, UCSC

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16
Q

What are SNPs?

A

Single nucleotide polymorphisms are unique genetic differences between individuals that contribute to the determination of human variation. (physical, behavior, disease, response to therapy)

17
Q

Mutation/ polymorphism db

A

They contain data on SNPs related usually to a specific disease. One general db: dbSNP

18
Q

Protein sequence db

A

UniprotKB : Swiss-prot + TrEMBL

NCBI-nr : Swiss-prot + GenPept + PIR + PDB + PRF + RefSeq

19
Q

What are Prot. domains and what do domain/family db contain?

A

Most proteins are formed by modular conserved structures. Databases contain information on domain signatires, from modelled sequence allignments.

20
Q

Some prot domain db?

A

Prosite, PRINTS, ProDom, Pfam, SMART, TIGRfam, DOMO, BLOCKS, CCD

21
Q

Proteomics db examples

A

Swiss2Dpage, Eco2Dbase, maize2Dbase

22
Q

Name the database of 3D structures

A

Protein Data Bank, it works by several servers

23
Q

What does a 3D structure db contains?

A

Spatial coordinates (x,y,z) of a macromolecule atoms whose structure has been defined experimentally. Most (90%) are proteins, but also, polysaccharides, RNA, viruses…..

24
Q

What do metabolic db contain?

A

Information describing enzymes, biochemical reactions and metabolic pathways

25
Q

Name metabolic db

A

MetaCyc
KEGG
Unipathway
Rhea

26
Q

Name nomenclature db

A

ENZYME, BRENDA

They store info on enzyme names and reactions

27
Q

What is the interactome?

A

Description of all protein/protein interactions in a sample

28
Q

What is Gene ontology?

What are the terms divided in?

A

A contolled vocab., standard terms used for indexing and retrieving information.

  • Biological process
  • Molecular function
  • Cellular component
29
Q

Whta should we consider when using a db?

A 
Quality of the data
Comprehensivenes
Update 
Redundancy
Indexation
Server quality (fast response)

Biostatistics (1 decks)

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