Lecture 8

Question 1

What are 3 features of UniProt?

Answer 1

Integrates:

• Sequence
• Structure
• Function data

Question 2

How do secondary databases enhance the PDB (Protein Data Bank)?

Answer 2

They add annotation about:

• Structure
• Function
• Evolution of protein domains

Question 3

What is the main obsticle in Natural Language Processing (NLP)?

Answer 3

Natural language is ambiguous and context dependent and requires syntactic analysis

Question 4

What is the result of machine pairwise associations?

Answer 4

Can form chains of reasoning

Question 5

What is indexing?

Answer 5

Extraction of possible search terms is compiled and searched in leu of full text which is too slow

Question 6

What are 3 issues with indexing?

Answer 6

• English/American spelling
• Synonyms
• Contamination (Such as author’s names being locations)

Question 7

What are 3 benefits of Electronic Lab Notebooks (ELNs)?

Answer 7

• Backed up
• Non-linear organisation
• Easily searchable

Question 8

What are 3 approaches of machine learning?

Answer 8

• Statistical techniques; clustering, classification, principle components analysis; Hidden Markov model
• Artificial Neural Networks; protein structure prediction, gene prediction
• Support Vector Machines; classification algorrithms

Question 9

What is BLAT?

Answer 9

Very rapid genomic sequence searching algorithm

Question 10

How do you avoid the challenge of synonyms?

Answer 10

Use of official and standardised names; ie the use of HGNC names is increasing