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2.1 Bioinformatics > Shane - Lecture 2 > Flashcards

Shane - Lecture 2 Flashcards

1
Q

Define homology

A

Shared ancestry

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2
Q

What are the two ways by which DNA sequences can have shared ancestry?

A

A speciation event

A duplication event

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3
Q

Define orthologs
(2)

A

Shared ancestry as a result of a speciation

Similar sequences often retain the same functions over the course of evolution

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4
Q

Define paralogs
(3)

A

Shared ancestry as a result of a duplication

Genes produced via gene duplication within a genome

Typically evolve new functions or become pseudogenes

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5
Q

What are pseudogenes?

A

Sequences which have evolved to not produce a functional product

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6
Q

What is our query in protein blast?

A

A protein

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7
Q

What are we searching for in BLASTp?

A

A similar protein

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8
Q

When is PSI-BLAST used?

A

To search for a distantly related protein

A position specific iterated blast

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9
Q

Comment on a result with an E value of 0.005

A

This is very close to zero
This is a meaningful result - didn’t occur by random

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10
Q

What is the most commonly used scoring matrix?

A

BLOSUM62

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11
Q

Comment on the use of E values for proteins vs with nucleotides

A

Don’t need to be as stringent

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12
Q

What percentage similarity does BLOSUM62 find?

A

Between 30 and 40 %

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13
Q

what does PSI stand for?

A

Position
Specific
Iterated

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14
Q

What is the E value cut off point for nucleotide sequences?

A

10x-6

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15
Q

What is the E value cut off point for protein sequences?

A

10x-3

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16
Q

How is PSI-BLAST different from pBLAST?
(4)

A

In PSI BLAST you first carry out your blast as normal

Then you repeat the search having selected only the sequences you want to carry forwards

This creates your own custom matric - Position Specific Scoring Matrix

This repeats until you find any new matches

17
Q

How does using a position specific scoring matrix work?

A

Uses collective similar characteristics of your selected identified sequences to find new related sequences

2.1 Bioinformatics (7 decks)

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