Category Archives: Bioinformatics

Bioinformatics

Talk on Hodgkin lymphoma cell graphs at ISMB 2016

It’s been a while since I went to the Intelligent Systems for Molecular Biology (ISMB) 2016 conference, but I thought I’d still share a few impressions.   The conference was held at a Disney Resort Hotel near Orlando, FL. Great … Continue reading

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Software to create a scientific poster for a conference

Scientific posters When starting your Ph.D., you will sooner or later go to a scientific conference to hear what others are doing, present your work and get to know the scientific community of your field. The slots for talks are … Continue reading

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Perl script to create a geometric graph from a set of 2D points

Here is another quick script by me. It is a Perl script which can be used to construct a geometric graph from a set of points P = {p1, p2, …} in 2D, using some edge threshold t. The points … Continue reading

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Algorithm to determine whether two strings are circular permutations of each other

A recent question on the string matching assignment sheet for the students: Design an algorithm that determines for two strings S and T (of equal length m)whether they are circular (or cyclic) permutations of each other. So what is a … Continue reading

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The Rabin-Karp string matching algorithm

The Rabin-Karp algorithm solves the string matching problem I described in an earlier post. Its worst-case running time is the same as for the naive string matching algorithm, but it performs significantly better on real-word inputs on average. (Note that … Continue reading

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Naive string matching

Note: This is an article in the string matching series. You can read the introduction to string matching here. All elaborated and fast string matching algorithms perform some kind of preprocessing to gain information on the pattern. This information is … Continue reading

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Algorithms for string matching

String matching I am responsible for a tutorial on Algorithms and Models in Computational Biology this semester, so I decided to write a bit about some of the algorithms here when ever I find the time. The posts here intentionally … Continue reading

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