L2

Question 1

What is the major challenge of the genomics era?

Answer 1

To store and handle terabytes (TB) of sequence data through the establishment and use of computer databases

Question 2

What is a database

Answer 2

A computerized archive used to store and organize data in such a way that information can be retrieved easily via a variety of search criteria

Question 3

What are databases made of?

Answer 3

Computer hardware and software for data management

Question 4

What should each record(entry) in a database contain?

Answer 4

A number of fields that hold the actual data items.

Question 5

What is the process of making a query

Answer 5

Process by which a user expects the computer to retrieve a whole data record by specifying a particular piece of info to be found in a particular field.

Question 6

What is knowledge discovery

Answer 6

A function of biological databases which refers to the identification of connections between pieces of information that were not known when the information was first entered

Question 7

Types of databases

Answer 7

• flat file format
• relational database management
• object-oriented database management systems

Question 8

What is a flat file format

Answer 8

A long text file that contains many entries separated by a delimeter (|)

Question 9

What are database management systems

Answer 9

Sophisticated computer software programs for organizing, searching and accessing data

Question 10

What are relational databases

Answer 10

They make us of a set of tables to organize data. They are created using a programming language known as structured query language (SQL)

Question 11

Each table in a relational database is also called

Answer 11

Relation which is made up of columns and rows. Columns represent individual fields. Rows represent values in the fields

Question 12

How is a query executed in a relational database

Answer 12

The system selects linked data items from different tables and combines the information into one report

Question 13

What are primary databases?

Answer 13

They are archives of raw proteins or DNA sequence data submitted by the scientific community

Question 14

Examples of primary databases

Answer 14

GenBank, Protein Data Bank (PDB)

Question 15

What databases does the International Nucleotide Sequence Database Collaboration made of?

Answer 15

-GenBank
-European Molecular Biology Laboratory (EMBL)
-DNA Data Bank of Japan (DDBJ)

Question 16

What is GenBank

Answer 16

The most complete collection of annotated nucleic acid sequence data for almost every known organism

Question 17

GenBank consists of

Answer 17

• DNA
• mRNA
• cDNA
• ESTs

Question 18

The Genpept database is for?

Answer 18

Protein sequences, majority of which are conceptual translations from DNA sequences

Question 19

What are the two ways to search for sequences in GenBank

Answer 19

• using text-based keywords
• using molecular sequences to search by sequence similarity using BLAST

Question 20

Functional divisions in GenBank

Answer 20

• EST
• GSS
• WGS
• ENV

Question 21

EST (expressed sequence tags)

Answer 21

Contains short single cDNA reads. Represent what is expressed in a given tissue at a particular development stage

Question 22

GSS (genome survey sequences)

Answer 22

Contains genomic sequences derived from random single-pass reads

Question 23

WGS (whole genome shotgun sequence)

Answer 23

Use a whole genome shotgun approach to gain large coverage with the caveat of large amounts of unassembled sequence

Question 24

ENV (environmental samples)

Answer 24

Contains sequences normally derived from a metagenomic sample

Question 25

Other functional divisions in GenBank

Answer 25

• PRI (primate sequences)
• ROD (rodent sequences)
• MAM (other mammalian sequences)
• PLN (plant, fungal and algal sequences)
• VRL (viral sequences)

Question 26

Similarity and difference in data contained in GenBank, EMBL, DDBJ

Answer 26

Similarity: data entered is identical, info regarding species, sequence length are entered via structure fields

Question 27

What is accession

Answer 27

Usually a single or two letters followed by five or six digits respectively (U12344)

Question 28

what is GI

Answer 28

If a sequence changes in any way, a new GI number will be assigned

Question 29

What is the FASTA file format

Answer 29

It is a sequence format because it contains plain sequence information

Question 30

What are secondary databases

Answer 30

They contain computationally processes sequence information derived from primary databases

Question 31

Example of a secondary database

Answer 31

SWISS-PROT. It provides detailed sequence annotation that includes structure, function and protein family assignment

Question 32

specialized databases

Answer 32

Serve a specific research community or focus on a particular organism

Question 33

Specialized databases include

Answer 33

• Flybase
• WormBase
• TAIR
• EcoCyc
• SGD

Question 34

What is Entrez

Answer 34

A biological database retrieval system which comes from cross-referencing between NCBI databases

Question 35

Disadvantages of biological databases

Answer 35

• overreliance on sequence information and related annotations without understanding the reliability of the information
• there can be many errors in sequence databases
• there are high levels of redundancy in primary sequence databases
• annotations of genes can also be false or incomplete