Exercise sheet 6: BLAST

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Exercise 1

You are given accession number NM_000667.3. Use the BLAST web server to find out about the gene that belongs to this accession number (choose nucleotide blast, and the database reference RNA sequences (refseq_rna)).

1a)

Which gene is it, and in which organism?

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Solution

Gene: Alcohol Dehydrogenase 1A

Organism: Homo sapiens (human)

1b)

Which other organisms does it seem to be highly conserved in?

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Solution

• Gorilla gorilla: gorilla
• Pan troglodytes: common chimpanzee
• Pan paniscus: bonobo
• Nomascus leucogenys: northern white-cheeked gibbon
• Cebus capucinus: white-headed capuchin

Many more…

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Exercise 2

You are given a nucleotide query sequence \(q\) = \(\texttt{ATAC}\), and a nucleotide database sequence \(s\) = \(\texttt{ATAAAACGGGGGG}\). The word-size \(k=2\). Use a simple scoring scheme that assigns a score of \(2\) for a match and a score of \(-1\) for a mismatch.

2a)

Generate all \(k\)-length words of the query sequence.

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Solution

• \(w_1=AT\)
• \(w_2=TA\)
• \(w_3=AC\)

2b)

List all possible words for the first \(k\)-length word (AT) that have a score of at least \(T_1=1\).

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Solution

• \(s(AA)=1\)
• \(s(AC)=1\)
• \(s(AG)=1\)
• \(s(AT)=4\)
• \(s(CT)=1\)
• \(s(GT)=1\)
• \(s(TT)=1\)

2c)

Scan the database for exact matches for the words from the question 2B.

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Solution

AA at position 2,3,4. AC at position 5, AT at position 0.

2d)

Extend the exact matches that you found in the question 2C to the left/right and report all MSPs with a score greater than \(4\).

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Solution

AA:

Pos: 2              ATA
                    |||
                    AAA     with score 3

Pos: 3              ATAC
                    ||||
                    AAAC    with score 5

Pos: 4              AT
                    ||
                    AA    with score 1

AT:

Pos: 0              ATA
                    |||
                    ATA     with score 6

AC:

Pos: 5              AT
                    ||
                    AC     with score 1

MSPs start in the template at index 0 and 3.

2e)

What happens if we vary the parameters k and \(T_1\)?

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Solution

• Higher \(T_1\), \(k\): - faster (less seeds), - less sensitive (some hits will be missed)
• Lower \(T_1\), \(k\): - slower (more seeds), - more sensitive (less hits will be missed)

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Exercise 3 - Programming assignment

For the programming tasks, please follow the instructions given in GitHub Classroom under the following link.

https://classroom.github.com/a/HoQv5vpm

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