General information

How to cite RegScan

RegScan Workgroup

RegScan  publications

User's guide

MATRIX

Description of:

Search for degenerate oligonucleotide motifs (ARGO)

ARGO_VIEW program

RecGroup program

RGSiteScan program

MMSite2 program

MultAlig program

Recog program

PolIIIScan program

NASCA

Complexity

ARGO

How to use ARGO program.

1. Type or paste set of your sequences into the window. Number of sequences should be less than 100 and length of sequences should be less than 100 b.p..

2. Set the length of oligonucleotides. Our method is based on the consideration of the complete vocabulary of the length L for each regulatory genome sequence and search for related oligonucleotides of the length l. We recommend to use 6< l <12.

3. Set the Hamming distance. The Hamming distance between two oligonucleotides, in our case, is number of not coinciding positions in these oligonucleotides.

    AATGCGT
    TAGGCTT
    *A**G**T  Hamming distance is equal to 5.

    If Hamming distance R between oligonucleotides from different sequences is lower than the threshold value ro, they are united into one class.

    We recommend to use ro >( l/2 ).

4. Set the minimal fraction of the regulatory genome sequences containing the motif.

5. Set the decimal logarithm of minimal significance level. The oligonucleotide motif is considered significant, if it meets the following conditions:
(1) the fraction f of the RGS containing the motif is higher than a certain level fo and
(2) the binomial probability P(n,N) to observe this motif by accidence in n and more number of RGS from N RGS considered, is lower than a significance level a.

We recommend to use lg(a)>-8.

6. Set the alphabet size used for building of oligonucleotide motifs.

7. Set the parameter allows or prohibits the search of motifs in complementary chains of DNA.

  • 8. Press "Submit".

  • 9. The result looks like a set of oligonucleotide motifs, founded in the region.

 

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