Databases (Week 2)

Question 1

1. Define “Bioinformatics”

Answer 1

Oxford: Management info system for molecular biology + practical applications

NCBI: Field of science in which biology, computer science + information technology
merge into 1 discipline. 3 subtypes
✓ Development of new algorithms + statistics to assess relationships among
data set
✓ Analysis + interpretation of data types including nucleotide + amino acid
sequences
✓ Development + implementation of tools that enable efficient access +
management of different information

Question 2

2. Difference between bioinformaticist and bioinformatician

Answer 2

Bioinformaticist: An expert that knows how to use bioinformatics tools + write
interfaces for effective use of tools. Designs + implements tools + makes use
complex algorithms

Bioinformatician: A trained individual who knows how to use bioinformatics tools
without a deeper understanding. Most biological scientists have a basic
understanding of underlying algorithms.

Question 3

3. Difference between information storage with regards to single sequences,
   features and annotations, as well as collections. Know examples thereof

Question 4

4. Define “database”

Answer 4

Database: A comprehensive collection of related data organized for convenient access, generally stored in computer.

Question 5

5.1 Raw Data (8)

Answer 5

1. Sequences = uploaded + maintained by those who submitted it
2. RAW
3. Redundant (unnecessary)
4. Level of info = sparse
5. Can represent incomplete records
6. Quality of data = unknown
7. Longevity can be indefinite
8. No automatic linking withother database

Question 6

5.2 Curated Data (6)

Answer 6

1. 3rd party that maintains it, who did not necessarily generate data
2. Originates from a primary database
3. Non – redundant (not unnecessary)
4. Created to extract extra information
5. Represents complete records
6. Linking with other databases

Question 7

5.3 Specialist Data (4)

Answer 7

1. Contains mix of Primary + Derived data of only select group or single species Maintained + updated by unofficial collaborators
2. Contains bulk Whole Genome Sequencing data which can be considered as primary
3. Contains reference sequences derived from multiple sequences
4. Restricted public access

Question 8

6. Difference between level of scope and level of curation of databases

Answer 8

Level of scope: Single, collection + features and annotations [SCFA]

Level of curation: Raw, curated and specialist [RCS]

Question 9

7. Examples of raw, curated and specialist databases

Question 10

8.1 Direct query (& PROBLEM)

Answer 10

1. Know exactly what is wanted
2. Each record in database has unique value = Accession number
3. Return results ONLY for that query. Unless database contains links to similar data

Problem: few databases share same accession
numbers + use same format

Question 11

8.2 Indirect query (4)

Answer 11

1. Generally know what is wanted
2. Can use different text queries such as gene names, organisms, products of genes
3. Multiple entries for 1 sequence you will receive multiple results
4. Meta data such as authors, date of publication can also be used

Question 12

8.3 Way to search with multiple queries:

Answer 12

• NCBI’s Entrez system: link out to other databases that might contain
different data of your match
• Return matches from multiple databases
• Boolean Operators
• AND, OR + NOT
• CAPITALS
• Multiple times in 1 query
• ….. AND …. OR …. NOT …. AND …. OR
• The NCBI’s Entrez system: certain info of records individually indexed
allowing you to search specifically for them
• Text qualifiers or Indexed terms 4
• Sequence length [SLEN]
• Organism [ORGN]
• Features [FKEY]
• Properties [PROP]
• gbdiv – GenBank division

Question 13

Data type refers to
AND
Single means

Answer 13

data type - different formats

single - that it is one data entry with more than one data type.

Question 14

9.1 FASTA Text format

Answer 14

FASTA (*. fa or *.fas or *.fasta)
• Simple text-based file format
• Edit with Notepad or any other basic text editor

• Used to download sequence info from records

• NO OTHER DATA PRESENT
• NO SEQUENCE FEATURES OR RECORD FEATURES
• Only 2 lines per record
• 1st line preceded with ‘>’ to denote name of record
• 2nd line sequence itself
• ONLY IUPAC nucleotide or amino acid letters

Question 15

9.2 GenBank Text format

Answer 15

flat file (*.gb)

• Complex file format that preserves ALL sequence information
• Sequence features + Meta data
• Not readably editable
• Cannot open with text editor.
• Allows interactive views of sequences when using programs that can accommodate them
• Multiple lines per record # of lines dependent on how much data is available