Oligo-nucleotide Scales

This program takes a nucleotide sequence and outputs oligo nucleotide sequences in order of composition score. The values for nucleotides, oligo length, and intercept are user editable. The steps taken to obtain the output are as follows:

  1. The input string is changed to all uppercase.
  2. Any non-nucleotide characters are removed and U's are replaced with T's
  3. Single Sequences are reverse complemented. Lists are left as entered.
  4. The sequence is then examined in oligo sized words. The values of each oligo are summed. Composition_Score is then computed by adding this sum to the Intercept value. The oligos are then displayed in order of Composition_Score.
  5. The "Oligo Length" field does nothing when processing a list.

Start and end coordinates refer to the reverse complement of the users input sequence.
Start and end coordinates are zero when processing a list.
Composition_Score = sum of the nucleotide values in oligo + Intercept value.
Hybridization_Intensity = EXP(Composition_Score) where EXP is the exponential function.

Tip:  This Application may run faster in Internet Explorer than Netscape.
Tested on Internet Explorer 6.02 & Netscape 6.2


This program was created at the University of Utah in the Gesteland & Atkins Labs
by Andy Hammer & Olga Mavteeva on 26 June 2003.

For more information mail: olgam@howard.genetics.utah.edu