Computer programs to help study the nuclear genome Flashcards

1
Q

What is BLAST?

A

Basic local alignment search tool

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2
Q

What does BLAST do?

A

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

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3
Q

What is the query in a BLAST search?

A

Your supplied sequence

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4
Q

What are the subjects/hits in a BLAST search?

A

The sequences from the database that match your query

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5
Q

What is the score in a BLAST search?

A

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

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6
Q

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

A

High

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7
Q

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

A

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

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8
Q

What is the E-value in a BLAST search?

A

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

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9
Q

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

A

Low

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10
Q

What is BLAT?

A

BLAST like alignment tool

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11
Q

What does BLAT do?

A

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

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12
Q

What is Homologene?

A

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

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13
Q

What is a homolog?

A

Genes that have a similar DNA sequence due to shared ancestry

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14
Q

What is an ortholog?

A

Genes that are similar between different species

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15
Q

What is a paralog?

A

Genes that are similar within the same organism

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16
Q

What is the ENCODE program?

A

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

17
Q

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

A

75%

18
Q

What is the G-value paradox?

A

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

19
Q

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

A

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

20
Q

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

A
  1. Exon skipping
  2. Intron retention
  3. Usage of alternative splice sites
  4. Mutually exclusive exons
21
Q

How many genes are in the human genome?

A

58 000

22
Q

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

A

19 800

23
Q

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

A

15 800

24
Q

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

A

7500

25
Q

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

A

15 000

26
Q

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

A

Much easier to study than RNA or pseudogenes