Computer programs to help study the nuclear genome

Question 1

What is BLAST?

Answer 1

Basic local alignment search tool

Question 2

What does BLAST do?

Answer 2

Takes a DNA or protein sequence and looks through several databases for similar sequences in all organisms

Question 3

What is the query in a BLAST search?

Answer 3

Your supplied sequence

Question 4

What are the subjects/hits in a BLAST search?

Answer 4

The sequences from the database that match your query

Question 5

What is the score in a BLAST search?

Answer 5

A number that describes the quality of alignment between the query and the subject

Question 6

Do you want a high or low score from a BLAST search?

Answer 6

High

Question 7

How is score influenced by the length of the query in a BLAST search?

Answer 7

Longer queries with perfect matches have a higher score than shorter queries with perfect matches, since longer queries will be more specific

Question 8

What is the E-value in a BLAST search?

Answer 8

Parameter that tells us how many hits we would get by chance

Question 9

Do you want a high or low E-value from a BLAST search?

Answer 9

Low

Question 10

What is BLAT?

Answer 10

BLAST like alignment tool

Question 11

What does BLAT do?

Answer 11

Takes a query sequence and searches databases for matching sequences from the same organism

Question 12

What is Homologene?

Answer 12

Search tool that looks for homologous sequences to your query in other organisms

Question 13

What is a homolog?

Answer 13

Genes that have a similar DNA sequence due to shared ancestry

Question 14

What is an ortholog?

Answer 14

Genes that are similar between different species

Question 15

What is a paralog?

Answer 15

Genes that are similar within the same organism

Question 16

What is the ENCODE program?

Answer 16

Encyclopedia of coding DNA elements. Is a functional annotation of the human genome that started in 2003 and is still running

Question 17

What percentage of the human genome has the potential to be transcribed over every tissue?

Answer 17

75%

Question 18

What is the G-value paradox?

Answer 18

The lack of correlation between gene number and the perceived complexity of the organism

Question 19

Why do humans actually code more proteins than the number of coding genes suggest?

Answer 19

Alternative transcripts. Each protein coding gene produces on average 6 transcripts, 4 of which can be translated

Question 20

What are 4 mechanisms by which alternative transcripts are generated by alternative splicing?

Answer 20

1. Exon skipping
2. Intron retention
3. Usage of alternative splice sites
4. Mutually exclusive exons

Question 21

How many genes are in the human genome?

Answer 21

58 000

Question 22

Out of the 58 000 genes in humans, how many genes are protein coding?

Answer 22

19 800

Question 23

Out of the 58 000 genes in humans, how many genes encode lncRNA?

Answer 23

15 800

Question 24

Out of the 58 000 genes in humans, how many genes encode small ncRNA?

Answer 24

7500

Question 25

Out of the 58 000 genes in humans, how many genes are pseudogenes?

Answer 25

15 000

Question 26

Why have we tended to hyperfocus on protein coding genes in studies?

Answer 26

Much easier to study than RNA or pseudogenes