Here’s a thought that first came to my head towards the end of last year, and I almost forgot about it, but Euan’s post where he asks “Don’t know if there are any other bioinformatics algorithms that have been applied to non-biological problems?” and my own recent discoveries about spam and bioinformatics re-kindled some thoughts, so here is a quick screencast on using multiple sequence alignment (as an illustration) for finding people in social networks.
The general idea is to use substitution matrices for an alphabet where each letter of the alphabet can be assigned some property of interest, e.g. favorite music type.
Crude, but worth a thought.
Technorati Tags: Screencast, Bioinformatics, Social Networking
4 Comments
I’d say that strictly speaking, there is no such thing as a “bioinformatics algorithm”. There are only algorithms, some of which have found application in bioinformatics. The oft-quoted BLAST algorithm, for instance, is an approximation of Smith-Waterman, which is a variation of Needleman-Wunsch and all of them are based in dynamic programming methods. You might say that they align characters in a pair of strings – which just happens to be applicable to biological sequences. Look also at the many statistical methods in bioinformatics – SVMs, HMMs, various kinds of discrimination analysis – they all had their roots elsewhere.
I think you still have an interesting question though – do methods commonly associated with bioinformatics have other uses?
Feeling tired and pedantic today…
I'd say that strictly speaking, there is no such thing as a “bioinformatics algorithm”. There are only algorithms, some of which have found application in bioinformatics. The oft-quoted BLAST algorithm, for instance, is an approximation of Smith-Waterman, which is a variation of Needleman-Wunsch and all of them are based in dynamic programming methods. You might say that they align characters in a pair of strings – which just happens to be applicable to biological sequences. Look also at the many statistical methods in bioinformatics – SVMs, HMMs, various kinds of discrimination analysis – they all had their roots elsewhere.
I think you still have an interesting question though – do methods commonly associated with bioinformatics have other uses?
Feeling tired and pedantic today…
Neil
You’re quite right. Should have said something like methods commonly used in Bioinformatics or something. Having written my share of dynamic programming algos that was a little sloppy on my part. The question remains. Do methods/techniques commonly used in the bioinformatics realm have applications in other areas.
Neil
You're quite right. Should have said something like methods commonly used in Bioinformatics or something. Having written my share of dynamic programming algos that was a little sloppy on my part. The question remains. Do methods/techniques commonly used in the bioinformatics realm have applications in other areas.