[BiO BB] Looking for researcher, to assist on blast-like invention
dwrice at indiana.edu
Tue Feb 12 01:49:24 EST 2008
If you have a way to speed up the full S&W algorithm it would be
interesting whether or not it is faster than BLAST. I would focus on
showing it is significantly faster than the current implementations of
the smith and waterman. Such an algorithm could be incorporated into
BLAST or any other dynamic programming algorithm. You can test it, for
example, by searching the swissprot database
ftp://ftp.ncbi.nih.gov/blast/db/swissprot.tar.gz with a bunch of queries
pulled from this database. It would seem, however, that you could
calculate the time savings directly as a function of conditions. You
shouldn't need any help with this. Just show it is significantly faster
than the S&W, while searching the entire matrix, and you are golden.
Theodore H. Smith wrote:
> Hi everyone,
> So I've been working, on and off, on this algorithm for quite a while
> now. It's basically an invention of mine. It is a "blast-like"
> algorithm, in that it does "Fuzzy lookup" operations across a database
> of letters. I am designing this algorithm to be useful for bio-
> informatics, this is the main field I am initially targetting.
> The database will be filled with protein sequences, and the search
> across the database will be another protein sequence. The algorithm
> has a "scoring matrix", which can accept different protein replacement
> scores. The cost of inserting letters (protein letters) can be
> configured also.
> In this sense, it's no different to Smith-Waterman. The same input,
> the same output!
> The real difference from Smith-Waterman, is it's speed. My algorithm
> will be hugely faster. This is because I use many techniques to avoid
> processing unnecessary parts of the Smith-Waterman matrix.
> I also use many tricks to reuse computations across various proteins.
> For example, the matrix for protein "ABCDE", is identical, at first
> anyhow, for the matrix for "ABCDEFG". This means if I have both
> proteins "ABCDE", and "ABCDEFG" in my protein database, I can test
> both of them against the search query, in almost half the time. My
> algorithm also runs in logarithmic-time with respect to the size of
> the database. Basically, bigger databases run disproportionately faster.
> I want to turn this algorithm, into something useful for people. My
> first challenge here, is to answer the question "is this algorithm
> faster, or better than BLAST". If it is not faster, my algorithm
> basically has little use. But I have good hopes it will be faster! I
> am very good with these sort of things, you see :) Speed is my strong-
> Currently, I do not know about the speed, because I haven't
> implemented a C++ version of my algorithm, or a good speed testing
> I do however know that my algorithm is more accurate than BLAST,
> because it is just as accurate as SSEARCH, as mine uses the Smith-
> Waterman algorithm. Whereas BLAST uses a heuristic, intelligent guess-
> work basically. A fine heuristic, but still a heuristic. Mine is
> methodological, not heuristic based.
> So here is what I am looking for!
> I am hoping, that someone in the field will be able to offer me
> guidance, interest, enthusiasm, suggestions and maybe even do some
> testing for me.
> Perhaps a student doing a bio-informatics related degree, who would
> like to write a paper on an alternative way of processing protein
> databases. My invention could be an interesting subject for a paper.
> Or perhaps a researcher who just has an interest in these sort of
> things! Perhaps a researcher who feels there must be a better way of
> doing these things. Or anyone really in this field with the time and
> interest, and feels helping me could help him (or her) too in some way.
> I'd like someone I can ask a lot of questions to, and show my software
> to, and explain my hopes what I can achieve with it.
> Basically, my first question to you, would be "how would I set this up
> to be useful for someone", and "how would I test it's usefulness, what
> would you need to know about my algorithm that you would decide to use
> it over blast"
> It's sort of a vague question from me, like "what do you need me to
> do", but... well that's where I am right now. Sort of a bit on the
> outside hoping someone on the inside will show me something.
> So it's an opportunity to tell me what you want, basically!! Tell me,
> and I might just make it.
> Who knows? Maybe one day in a few years time, everyone will be using
> this "ElfDataFuzzy" algorithm that I invented, instead of BLAST! You
> might be part of something.
> Thanks to anyone who replies!
> "String processing, done right"
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> BBB at bioinformatics.org
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