In Part 1 of this post we discussed a data structure called a de Bruijn graph and covered its application to genome assembly. To summarize, a de Bruijn graph is a type of graph that represents a set of k-mers as a set of directed edges on …
Posted in Computational Biology
To provide a bit of context for a discussion of Euler paths and Euler cycles: starting around December, a group of us in the Lab for Data Intensive Biology (DIB Lab) started working through the textbook Bioinformatics Algorithms: An Active Learning Approach and the associated website, Rosalind.info.
Rosalind.info is a site that is similar in style …
This is Part 3 of an N-part series.
The Josephus Problem for a …
This is Part 2 of an N-part series.
In this blog post we'll walk through two examples of …
This is Part 1 of an N-part series.
The following problem, Cat and Mice, is Puzzle 88 in Boris Kordemsky's The Moscow Puzzles.
Purrer has decided to take a nap. He dreams …
In Volume 4 Fascicle 0 of Donald Knuth's Art of Computer Programming, Knuth introduces a tool for exploring concepts in graph theory: the five-letter words. This is a collection …
In Volume 4, Facsimile 0 of Donald Knuth's Art of Computer Programming, in which Knuth covers graph theory, he introduces a list of five-letter words as part of a data set useful in exploring graph theory and graph algorithms.
The list of words is part of the Stanford Graph Base, a set of data sets that are useful for studying graph theory and networks.
See Five Letter Words on the charlesreid1.com wiki for details.
This post …
Posted in Computer Science
NOTE: The code covered in this post uses Python 3. The scripts can be converted to Python 2 with minimal effort, but the author would encourage any user of Python 2 to "put on your big kid pants" and make the switch to Python 3. Let's all make this painful, drawn-out switch from Python 2 to Python 3 a thing of the past, shall we?
The letter/word coverage problem, as presented by Donald Knuth in Volume 4, Facicle 0 of his masterpiece Art of …
NOTE: The code covered in this post uses Python 3. The scripts can be converted to Python 2 with minimal effort, but the author would encourage any user of Python 2 to "put on your big kid pants" and make the switch to Python 3. Let's all make this painful, drawn-out switch from Python 2 to Python 3 a thing of the past, shall we?
NOTE: The code covered in this post uses Python 3. The scripts can be converted to Python 2 with minimal effort, but the author would encourage any user of Python 2 to "put on your big kid pants" and make the switch to Python 3. Let's all make this painful, drawn-out switch from Python 2 to Python 3 a thing of the past, shall we?