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Assignment 11 Due: 25 January 2016, 8 Am: Bioinformatics I WS 2016/17

This document provides instructions for an assignment in a bioinformatics course. It asks students to implement the shift-and algorithm and Horspool algorithm to search for matches between sequences in two files, and to analyze whether Horspool is better suited for short protein queries or long DNA queries. It is due on January 25th, 2016 at 8 am.

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Anton Melcher
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53 views1 page

Assignment 11 Due: 25 January 2016, 8 Am: Bioinformatics I WS 2016/17

This document provides instructions for an assignment in a bioinformatics course. It asks students to implement the shift-and algorithm and Horspool algorithm to search for matches between sequences in two files, and to analyze whether Horspool is better suited for short protein queries or long DNA queries. It is due on January 25th, 2016 at 8 am.

Uploaded by

Anton Melcher
Copyright
© © All Rights Reserved
We take content rights seriously. If you suspect this is your content, claim it here.
Available Formats
Download as PDF, TXT or read online on Scribd

Prof.

Daniel Huson
Caner Bagci
Anna Gorska
Zentrum fur Bioinformatik
Fachbereich Informatik
Mathematisch-Naturwissenschaftliche Fakultat

Bioinformatics I WS 2016/17

Assignment 11 Due: 25th January 2016, 8 am

1 Shift-And algorithm (4 points)

Implement the shift-and algorithm as discussed in the lecture.


Apply to the files assignment11-text.fasta and assignment11-query.FASTA, available from the
course website.

2 Horspool algorithm (5 points)

Implement the Horspool algorithm, as discussed in the lecture.


Apply to the files assignment11-text.fasta and assignment11-query.FASTA, , available from the
course website.

3 Horspool on protein vs DNA (1 point)

Is the Horspool algorithm more suitable for short protein queries or for long DNA queries, and why?

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