[BiO BB] Looking for researcher, to assist on blast-like invention

Martin Gollery marty.gollery at gmail.com
Mon Feb 11 17:51:15 EST 2008

The first step is to implement it in C++ to see how fast it is. Once
you have an executable, testing it will be relatively straightforward.


On Feb 11, 2008 8:21 AM, Theodore H. Smith <delete at elfdata.com> 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-
> point.
> Currently, I do not know about the speed, because I haven't
> implemented a C++ version of my algorithm, or a good speed testing
> framework.
> 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!
> --
> http://elfdata.com/plugin/
> "String processing, done right"
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Martin Gollery
Senior Bioinformatics Scientist
TimeLogic- a Division of Active Motif
880 Northwood Blvd. Suite 7
Incline Village, NV 89451

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