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    Archive for September 13th, 2006

    A ton of humour

    13th September 2006

    Sitting late in the night in front of my PC, and doing something boring, I stumbled upon the albinoblacksheep website. The two things I read were Cyber Sex (with a kind of follow-up) and probably old but anyway funny Automation: A Way of the Past – I liked that, so here’re the links :) .
    And if you’re Star Wars fan – you MUST watch ASCII Star Wars, for the Force to stay with you ;-)

    I didn’t read anything else there, but looks like a funny resource.

    Hope you will enjoy :)

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    Posted in Notepad, Web | No Comments »

    PFM2PWM: which “nucleotide background frequency” to use

    13th September 2006

    As I previously mentioned, in converting PFM to PWM single variable – [prior] background nucleotide frequency – was ambiguous to me. From other articles I noticed that it is usually set to 0.25 (1/4 – because there 4 nucleotides, thus in “perfectly random” sequence they would appear in 25% of cases each). In that post, I also thought of using “real” background frequency of nucleotides, calculated from the sequence, to which the matrix is to be applied.

    I wrote a program to search all the 1000-basepair upstream sequences from all human, rat and mouse genes, present in Ensembl database release 40 (assuming those 1kb upstreams to be “promoters” of genes). For each promoter, only the single best score was returned. Then I draw a graph of the distribution of the number of promoters (y-axis) depending on the best match scores (x-axis). I did the search twice – one with p(b) = 0.25, and one with p(b) set to calculated values of A/C/G/T content in each promoter.
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    Posted in Bioinformatics | 1 Comment »