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Comp Bio > Access to Sequenced Data and Related Information > Flashcards

Access to Sequenced Data and Related Information Flashcards

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Biology 101 flashcards
1
Q

Library of related information

  • collection & and preservation, easy access, standardized data presentation, minimize redundancy, data independence, management, updating, and organizing data into knowledge
A

BIOLOGICAL DATABASES

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2
Q

3 Main Nucleotide Sequence Database

A

GenBank
European Nucleotide Archive
DNA Database of Japan

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3
Q

National Center for Biotechnology Information (NCBI) of the National Institutes of Health (NIH) in Bethesda

A

GenBank

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4
Q

European Molecular Biology Laboratory (EMBL)-Bank Nucleotide Sequence Database at the European Bioinformatics Institute (EBI) in Hinxton, England

A

European Nucleotide Archive

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5
Q

National Institute of Genetics in Mishima

A

DNA Database of Japan

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6
Q

Other Common Biological Database

A

PubMed
UCSC
Genome Browser
e!Ensembl
FlyBase
UniProt
WormBase
GENEONTOLOGY
RCSB PROTEIN DATA BANK
tair
Rice Genome Annotation Project
Kyoto Encyclopedia of Genes and Genomes (KEGG)

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7
Q

Integration of Biological Databases

Challenges:
1. Database architecture = similar structure
2. How to access & what can be accessed data surfing
3. Naming system (S. cerevisiae RAD24 =rad17 in S. pombe)
4. Clash of concepts = definitions of terms (definition of GENE)

A
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8
Q

Integration of Biological Databases
Approaches:

A

Link Integration
View Integration
Data Warehousing

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9
Q

Integration of Biological Databases
Approach wherein:

▪ researchers begin their query with one data source and then follow hypertext links to related information in other data sources
▪ Vulnerable to naming clashes and ambiguities, updates, researcher-dependent

A

Link Integration

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10
Q

Integration of Biological Databases
Approach wherein:

▪ leaves the information in its source databases but builds an environment around the databases that makes them all seem to be part of one large system
▪ didn’t perform as well as the source database

A

View Integration

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11
Q

Integration of Biological Databases
Approach wherein:

▪ bringing all the data under one roof in a single database
▪ Issue on keeping the data warehouse up to date

A

Data Warehousing

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12
Q

What technique transforms the contents of multiple source databases to common data model. It then integrates the source data into a single large database.

A

Data warehouse technique

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13
Q

Types of Biological Data

A

Genomic Databases
RNA Databases
Protein Databases

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14
Q

Genomic Databases (3)

A

Sequenced Tag Sites (STS)
Genome Survey Sequences (GSSs)
High-Throughput Genomic Sequence (HTGS)

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15
Q

which genomic database?

= short (typically 500 base pairs long)
genomic landmark sequences

A

Sequenced Tag Sites (STS)

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16
Q

Which genomic database?

= consist of sequences that are genomic in origin

A

Genome Survey Sequences (GSSs)

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17
Q

Which genomic database?

= contains unfinished DNA sequences from sequencing centers

A

High-Throughput Genomic Sequence (HTGS)

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18
Q

Which RNA database?

= contain sequence data on “single-pass” cDNA sequences

A

Expressed Sequence Tags (ESTs)

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19
Q

Which RNA database?

= (unique gene) created for gene-oriented clusters by making nonredundant sets of ESTs

A

UniGene

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20
Q

Which protein database?

is the most comprehensive, centralized
protein sequence catalog

A

UniProt (aka Universal Protein Resource)

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21
Q

RNA Databases (2)

A

Expressed Sequence Tags (ESTs)
UniGene

22
Q

Key databases of UniProt:

A

Swiss-Prot
TrEMBL
PIR

23
Q

key database under UniProt

= considered the best-annotated protein database (structure and function)

A

Swiss-Prot

24
Q

Key database under UniProt

= translated EMBL-NSDL provides automated annotations of proteins

A

TrEMBL

25
Q

Key database under UniProt

maintains the Protein Sequence Database curated also by experts

A

PIR (aka Protein Information Resource)

26
Q

Key database layers under UniProt (3)

A

UniProtKB
UniRef
IniParc

27
Q

Key database layer under UniProt

the central database of either manual or automated annotations

A

UniProtKB (UniProt Knowledgebase)

28
Q

Key database layer under UniProt

offer nonredundant reference clusters on UniProtKB

A

UniRef (UniProt Reference Clusters)

29
Q

Key database layer under UniProt

consists of a stable, nonredundant archive of protein sequences

A

UniParc (UniProt Archive)

30
Q

Central Bioinformatics Resource (2)

A

National Center for Biotechnology Information (NCBI)
European Bioinformatics Institute (EBI)

31
Q

Central Bioinformatics Resource

  • creates public databases
  • conducts research in comp. biology
  • develops software tools for analyzing genome data
  • disseminates biomedical information
A

National Center for Biotechnology Information (NCBI)

32
Q

Central Bioinformatics Resource

  • Comparable to NCBI in its scope and mission
  • Represents a complementary, independent resource
  • Have six (6) core molecular databases
A

European Bioinformatics Institute (EBI)

33
Q

A database providing information on the structure of assembled genomes, assembly names and other meta-data, statistical reports ,and links to genomic sequence data

A

Assembly

34
Q

Finds regions of similarity between biological sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance.

A

BLAST

35
Q

a molecular biology database system that provides integrated access to databases

A

Entrez

36
Q

Boolean Operators:

A

AND, OR, NOT

37
Q

What searching database punctuation should be used to find specific phrase

A

Quotation marks “ “

38
Q

What searching database punctuation should be used to process as a unit rather than sequentially

A

Parenthesis ( )

39
Q

What searching database punctuation should be used for truncating query that begins/ends with a particular text string

A

Asterisk*

40
Q

a string of about 4–12 numbers and/or alphabetic characters that are associated with a molecular sequence record/expression/structure

A

Accession Numbers

41
Q

assigned consecutively to each sequence that is processed

A

GenInfo Number (GI:12345678)

42
Q
  • provide the best representative sequence for each normal (i.e., nonmutated) transcript produced by a gene and for each normal protein product
  • are curated by the staff at NCBI and are nearly nonredundant
A

Reference Sequence (RefSeq) Project

43
Q

define genomic sequences that can be used as reference standards for genes, representing a standard allele

A

Locus Reference Genomic (LRG) Project

44
Q

was established to identify a core set of protein-coding sequences that provide a basis for a standard set of gene annotations; “gold standards” of best-supported gene and protein annotations

A

Consensus Coding Sequence (CCDS) Project

45
Q

Offers high-quality, manual (expert) annotation of the human and mouse genomes, as well as selected other vertebrate genomes

A

Vertebrate Genome Annotation (VEGA) Project

46
Q

databases with a graphical interface representing sequence information and other data as a function of position across the chromosomes

A

Genome Browsers

47
Q

Principal genome browsers are:

A
  1. University of California, Santa Cruz (UCSC) Genome browser
  2. Ensembl Genome browser
  3. Map Viewer at NCBI
48
Q

Genome browser

  • supports the analysis of dozens of vertebrate and invertebrate genomes
  • provides graphical views of chromosomal locations at various levels of resolution
  • Each chromosomal view is accompanied by horizontally oriented annotation tracks
A

University of California, Santa Cruz (UCSC) Genome browser

49
Q

Genome browser

offers a series of comprehensive websites emphasizing a variety of eukaryotic organisms

A

Ensembl Genome browser

50
Q

Genome browser

includes chromosomal maps for a variety of organisms
(1) Home page, (2) genome view, (3) map view,(4) sequence view

A

Map Viewer at NCBI

Comp Bio (8 decks)

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