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Gene finding
Gene finding with similarity
Gene finding in Bacteria
Gene finding in Viruses
Next Generation
Gene search
Gene explorer
Protein location
RNA structure
Protein structure
Multiple alignment
Analysis of expression data
Plant promoter database
Search and map repeats
Extracting known SNPs



RULES for creating USER's set of REs:

1. USER's set must include only sequences of real REs and/or their consensuses.

2. Every real RE/consensus is described in 3 lines:
   LINE 1: Name/description of RE/consensus
   LINE 2: Sequence of of RE/consensus
   LINE 3: <par1> <par2> <par3> <par4>

3. Sequence (LINE2) may include both standard nucleotides (A/a, T/t, G/g,C/c) and their any combinations in according to IUPAC abbreviations:R - A or G, Y - T or C, K - G or T, M - A or C, S - G or C, W - A or T, B - G or T or C, D - A or G or T, H - A or C or T, V - A or G or C, N - A or G or C or T.
In the case of composite REs, 2 boxes are seperated by "-".
Length of RE/consensus sequence must not exceed 80 symbols, including "-" in the case of composite elements.
Capital letters indicate Conservative nucleotides (positions) in which mismatch is not allowd.

4. In LINE 3:
  <par1> - a maximal number of mismatches for the 1st box
  <par2> - a maximal number of mismatches for the 2nd box (for composite REs)
  If RE contains a single box, then <par2> = 0;
  If any mismatch is not allowed, then <par1> = <par2> = 0 )

  <par3> - minimal distance between boxes of composite RE
  <par4> - maximal distance between boxes of composite RE (for a single-box REs <par3> = <par4> = 0 )

All <par1>, <par2>, <par3> and <par3> are given as INTEGER in 4i5 format.

Example of USER's set of 3 REs:

RE 1  
    2    0    0    0
    1    1    8   10
RE 3  
    0    0    0    0
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