Algorithms on strings, trees, and sequences

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• ahelwer · Mar 30, 2012 · Recommends

  …seeing a video of ATP synthase in action [1]. Now, I know stuff like that doesn't have a lot to do with what is done in computational biology, but it did fire the imagination. I'm working my way through Algorithms on Strings, Trees, and Sequences - Computer Science and Computational Biology by Dan Gusfield [2], and have implemented (with tests) all of the algorithms encountered thus far in addition to some of the exercises [3]. So far, I really…

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• rickbradley · Jun 4, 2014 · Recommends

  This appears to be just reinvention of known algorithms on suffix trees. I recommend (and recommended as a comment on the original article) Dan Gusfield's book "Algorithms on Strings, Trees, and Sequences" which does a pretty thorough job of covering the relevant algorithms and data structures.

  on “Compressing Scrabble Dictionaries” ↗
• ahelwer · Apr 12, 2012 · Recommends

  I've not read that textbook, but another excellent text is "Algorithms on Strings, Trees, and Sequences" by Dan Gusfield (http://www.amazon.ca/Algorithms-Strings-Trees-Sequences-Comp...). It has a strong bioinformatics leaning, so you learn all sorts of interesting near-real-world applications for the algorithms.…

  on “Ukkonen's suffix tree algorithm explained in plain English” ↗
• stillworks · Oct 15, 2016 · Recommends

  …decreasing order of "easiness") - Python Algorithms - The Algorithm Design Manual - CLRS - Algorithms in Java (somehow I found CLRS easier to follow than this) - And then I found this recently, "Algorithms on Strings,Trees and Sequences: Computer Science and Computational Biology" (one should have at least gone through the first two recommendations before starting with this one to make it easier to read this one) Disclaimer : I have…

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• mcswell · May 14, 2024 · Mentions

  Dan Gusfield wrote a book in 1997 entitled "Algorithms on strings, trees and sequences: Computer Science and Computational Biology". We (what was then the Center for Advanced Study of Language at the University of Maryland) found some of the techniques described there to be useful in (natural)…

  on “A review on protein language models” ↗
• palaiologos · Feb 1, 2025 · Mentions

  …length /of the pattern/ - i.e. O(p). The suffix tree stores all suffixes of a string in a compressed manner (i.e. it has a linear space overhead, approximately O(20n) as given by Gusfield, D. (1997). Algorithms on Strings, Trees and Sequences: Computer Science and Computational Biology. Cambridge University Press), so you can search for a word in it by simply traversing from the root node to an internal or leaf node by following a sequence…

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• revertts · Mar 26, 2012 · Mentions

  To me, a lot of this divide is between books I read cover to cover and books I consider references or pick up for very specific sections (like "Algorithms on Strings, Trees and Sequences"). CLRS, TAOCP, and Gang of Four are all books I haven't read in their entirety, but have been indispensable for certain topics. I still recommend them to people all the time, and feel perfectly justified…

  on “Books Programmers Don't Really Read But Recommend” ↗